https://nesgwiki.chem.buffalo.edu/index.php?action=history&feed=atom&title=Resonance_Assignment%2FAbacus%2FFMCGUI_commandsResonance Assignment/Abacus/FMCGUI commands - Revision history2026-09-23T01:37:42ZRevision history for this page on the wikiMediaWiki 1.43.9https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/FMCGUI_commands&diff=3483&oldid=prevAgutmana: moved FMCGUI commands to Resonance Assignment/Abacus/FMCGUI commands2010-01-05T23:33:32Z<p>moved <a href="/index.php/FMCGUI_commands" class="mw-redirect" title="FMCGUI commands">FMCGUI commands</a> to <a href="/index.php/Resonance_Assignment/Abacus/FMCGUI_commands" title="Resonance Assignment/Abacus/FMCGUI commands">Resonance Assignment/Abacus/FMCGUI commands</a></p>
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</td></tr></table>Agutmanahttps://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/FMCGUI_commands&diff=2945&oldid=prevAlexLemak at 00:09, 3 December 20092009-12-03T00:09:24Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''Structure&gt;Water refinement&gt;calculate''' ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''Structure&gt;Water refinement&gt;calculate''' ===</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><div>&nbsp;''':''':&nbsp; Set up water refinement calculations</div><div>&nbsp;</div><div>''Prerequisites'':&nbsp;</div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ♦&nbsp;&nbsp; structure calculation with CYANA should be done</div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ♦&nbsp;&nbsp; ''Optional:''</div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ♦&nbsp;&nbsp; RDC data in PALES format.</div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ♦&nbsp;&nbsp; file with ZN ion ligands (file “zn_ligands” )</div><div>&nbsp;&nbsp;&nbsp;&nbsp; <br></div><div>&nbsp;[[Image:Fmcgui fig2.18.jpg|thumb|right|400px]]<br> </div> <div>User will be asked to&nbsp;:</div> </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><div>&nbsp;''':''':&nbsp; Set up water refinement calculations</div><div>&nbsp;</div><div>''Prerequisites'':&nbsp;</div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ♦&nbsp;&nbsp; structure calculation with CYANA should be done</div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ♦&nbsp;&nbsp; ''Optional:''</div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ♦&nbsp;&nbsp; RDC data in PALES format.</div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ♦&nbsp;&nbsp; file with ZN ion ligands (file <ins style="font-weight: bold; text-decoration: none;">[[FMCGUI_commands#Structure.3EAdd_ZN_ligands|</ins>“zn_ligands”<ins style="font-weight: bold; text-decoration: none;">]] </ins>)</div><div>&nbsp;&nbsp;&nbsp;&nbsp; <br></div><div>&nbsp;[[Image:Fmcgui fig2.18.jpg|thumb|right|400px]]<br> </div> <div>User will be asked to&nbsp;:</div> </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*&nbsp;specify the name of directory for water refinement calculations,&nbsp; WATDIR; </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*&nbsp;specify the name of directory for water refinement calculations,&nbsp; WATDIR; </div></td></tr>
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</table>AlexLemakhttps://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/FMCGUI_commands&diff=2879&oldid=prevAlexLemak at 19:43, 2 December 20092009-12-02T19:43:36Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div></div><div>&nbsp;::&nbsp; Save the&nbsp;current state of the project</div><div>&nbsp;</div><div>What is currently in the computer memory is saved in the file PROJECTNAME.prj located in the root directory of the project. </div><div>&nbsp;</div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div></div><div>&nbsp;::&nbsp; Save the&nbsp;current state of the project</div><div>&nbsp;</div><div>What is currently in the computer memory is saved in the file PROJECTNAME.prj located in the root directory of the project. </div><div>&nbsp;</div> </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''<span>Poject&gt;Quit</span>''' ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''<span>Poject&gt;Quit</span>''' ===</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><div>:: Save the current state of the project and quit. </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"><div>&nbsp;&nbsp; </div></ins><div>:: Save the current state of the project and quit.<ins style="font-weight: bold; text-decoration: none;"></div><div>&nbsp;&nbsp; </div></ins></div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Data Menu<br> ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Data Menu<br> ==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>The DATA section serves to load&amp;save the data (such as protein sequence and peak lists). Since there are different formats of data-files that could be loaded in memory or saved on disk, one can use this section as format converter as well.</div><div>&nbsp;</div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>The DATA section serves to load&amp;save the data (such as protein sequence and peak lists). Since there are different formats of data-files that could be loaded in memory or saved on disk, one can use this section as format converter as well.</div><div>&nbsp;</div> </div></td></tr>
</table>AlexLemakhttps://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/FMCGUI_commands&diff=2854&oldid=prevAlexLemak at 18:42, 2 December 20092009-12-02T18:42:41Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>''':''': Display and analize assignment results </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>''':''': Display and analize assignment results </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><div>&nbsp;</div><div>The user is asked to select a directory were assignment probabilities were calculated (sa_run# or rem_run#). </div><div>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div>[[Image:Fmcgui_fig2.22.jpg|thumb|left|445px]][[Image:Fmcgui_2.24a.jpg|thumb|right|445px]]</div><div></div><div></div><div>&nbsp;<br></div><br> </del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><div>&nbsp;</div><div>The user is asked to select a directory were assignment probabilities were calculated (sa_run# or rem_run#). </div><div>&nbsp;New “Assignments Graphs” (AG) window pops up (see Figure 1<ins style="font-weight: bold; text-decoration: none;">, left</ins>). This window provides user with graphical means to manipulate&nbsp;PB fragment’s assignments without making changes of assignment status of PB fragments in memory. The current fragment’s assignment, taken from the memory, altogether with different scores associated with this assignment is shown when AG window is opened. The fragments that currently are not assigned are also shown in the bottom-right part of the AG window. User can modify the current assignment and to observe the resulting changes in the scores.</div><div><ins style="font-weight: bold; text-decoration: none;">[[Image:Fmcgui fig2.22.jpg|thumb|</ins>left<ins style="font-weight: bold; text-decoration: none;">|445px]][[Image:Fmcgui 2</ins>.<ins style="font-weight: bold; text-decoration: none;">24a</ins>.<ins style="font-weight: bold; text-decoration: none;">jpg|thumb|right|445px]]</ins></div><div></div><div></div><div>&nbsp;<br></div></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"><br> </del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"><div></del>New “Assignments Graphs” (AG) window pops up (see Figure 1). This window provides user with graphical means to manipulate&nbsp;PB fragment’s assignments without making changes of assignment status of PB fragments in memory. The current fragment’s assignment, taken from the memory, altogether with different scores associated with this assignment is shown when AG window is opened. The fragments that currently are not assigned are also shown in the bottom-right part of the AG window. User can modify the current assignment and to observe the resulting changes in the scores. </div><div><del style="font-weight: bold; text-decoration: none;">&nbsp;A particular fragment’s assignment is displayed on the </del>left <del style="font-weight: bold; text-decoration: none;">part of the AG window</del>. <del style="font-weight: bold; text-decoration: none;">The graph at the bottom shows ID of fragments assigned to each sequence position, while four graphs on the top show different scores that correspond to this assignment, namely, HNCA score, NOE scores, typing and assignment probabilities that currently loaded in memory</del>. <del style="font-weight: bold; text-decoration: none;">The scroll bar at the bottom allows user to move along protein sequence.&nbsp; <br></div><div>&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>&nbsp;&nbsp;&nbsp; <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br></div><div><br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </del></div><div><del style="font-weight: bold; text-decoration: none;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </del></div><div><del style="font-weight: bold; text-decoration: none;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </del></div><div><del style="font-weight: bold; text-decoration: none;">&nbsp;</del>&nbsp; <br><del style="font-weight: bold; text-decoration: none;"></div><div>In order to modify the assignment user have first to select protein sequence segment of interest by clicking on IDs of two residues that correspond to the edges of the segment. The colour of these residues, for example K56 and D59, will change to red (see Figure 2).&nbsp;Then pressing on “Select Segment” bar at the bottom of AG window will result in possible assignment for the selected window to be shown on top-right corner of AG window.&nbsp;The possible assignments for the selected sequence segment are taken form the selected directory shown on the title bar and correspond to sub-optimal fragment assignments sampled during SA or REM calculations.</div><div>&nbsp;</div><div>&nbsp;</del></div> </div></td><td colspan="2" class="diff-side-added"></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><div>The new assignment for the sequence segment should be selected from the list of possible assignments using mouse. The color of the selected line will turn red (see Figure 2.23). In the case user want to consider an assignment that is not present in the list, he should select any assignment from the list ant modify it by pressing the button “Edit” at the bottom of the AG window. A new window “Edit Assignment” pops up, and user can modify the assignment by typing changes in this window see Figure <del style="font-weight: bold; text-decoration: none;">3</del>). </div><div>&nbsp; &nbsp; <br></div><div><del style="font-weight: bold; text-decoration: none;">[[Image:Fmcgui fig2.24.jpg|thumb|right|250px]]</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</del><br> </div> <div>Once a new assignment for the sequence segment is selected the current fragments assignment shown on the left part of AG window can be modified by pressing button “Update” &nbsp;(see Figure <del style="font-weight: bold; text-decoration: none;">2</del>.25<del style="font-weight: bold; text-decoration: none;">)</del></div><div>&nbsp;</div> </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"><div><br> </div><div>&nbsp;A particular fragment’s assignment is displayed on the left part of the AG window. The graph at the bottom shows ID of fragments assigned to each sequence position, while four graphs on the top show different scores that correspond to this assignment, namely, HNCA score, NOE scores, typing and assignment probabilities that currently loaded in memory. The scroll bar at the bottom allows user to move along protein sequence.&nbsp; <br></div><div>&nbsp;&nbsp;&nbsp;&nbsp;<br></div><div>In order to modify the assignment user have first to select protein sequence segment of interest by clicking on IDs of two residues that correspond to the edges of the segment. The colour of these residues, for example K56 and D59, will change to red (see Figure 1,right).&nbsp;Then pressing on “Select Segment” bar at the bottom of AG window will result in possible assignment for the selected window to be shown on top-right corner of AG window. <div>[[Image:Fmcgui fig2.24.jpg|thumb|right|250px]]</div></div></ins><div><ins style="font-weight: bold; text-decoration: none;">The possible assignments for the selected sequence segment are taken form the selected directory shown on the title bar and correspond to sub-optimal fragment assignments sampled during SA or REM calculations. </ins>The new assignment for the sequence segment should be selected from the list of possible assignments using mouse. The color of the selected line will turn red (see Figure 2.23). In the case user want to consider an assignment that is not present in the list, he should select any assignment from the list ant modify it by pressing the button “Edit” at the bottom of the AG window. A new window “Edit Assignment” pops up, and user can modify the assignment by typing changes in this window see Figure <ins style="font-weight: bold; text-decoration: none;">2</ins>). </div><div>&nbsp; &nbsp; <br></div><div><br> </div> <div>Once a new assignment for the sequence segment is selected the current fragments assignment shown on the left part of AG window can be modified by pressing button “Update” &nbsp;(see Figure <ins style="font-weight: bold; text-decoration: none;">3)</div><div>[[Image:Fmcgui_fig2</ins>.25<ins style="font-weight: bold; text-decoration: none;">.jpg|thumb|center|500px]]</ins></div><div>&nbsp;</div></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">&lt;/div&gt;</del></div></td><td colspan="2" class="diff-side-added"></td></tr>
</table>AlexLemakhttps://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/FMCGUI_commands&diff=2850&oldid=prevAlexLemak at 18:34, 2 December 20092009-12-02T18:34:25Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 18:34, 2 December 2009</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>''':''': Display and analize assignment results </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>''':''': Display and analize assignment results </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><div>&nbsp;</div><div>The user is asked to select a directory were assignment probabilities were calculated (sa_run# or rem_run#). </div><div>&nbsp;</div><div><del style="font-weight: bold; text-decoration: none;">&nbsp;</del>[[Image:Fmcgui_fig2.22.jpg|thumb|right|<del style="font-weight: bold; text-decoration: none;">500px</del>]]</div><br></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><div>&nbsp;</div><div>The user is asked to select a directory were assignment probabilities were calculated (sa_run# or rem_run#). </div><div>&nbsp;</div><div>[[Image:Fmcgui_fig2.22<ins style="font-weight: bold; text-decoration: none;">.jpg|thumb|left|445px]][[Image:Fmcgui_2.24a</ins>.jpg|thumb|right|<ins style="font-weight: bold; text-decoration: none;">445px</ins>]]<ins style="font-weight: bold; text-decoration: none;"></div><div></div><div></div><div>&nbsp;<br></ins></div><br> </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><div>New “Assignments Graphs” (AG) window pops up (see Figure 1). This window provides user with graphical means to manipulate&nbsp;PB fragment’s assignments without making changes of assignment status of PB fragments in memory. The current fragment’s assignment, taken from the memory, altogether with different scores associated with this assignment is shown when AG window is opened. The fragments that currently are not assigned are also shown in the bottom-right part of the AG window. User can modify the current assignment and to observe the resulting changes in the scores. </div><div>&nbsp;A particular fragment’s assignment is displayed on the left part of the AG window. The graph at the bottom shows ID of fragments assigned to each sequence position, while four graphs on the top show different scores that correspond to this assignment, namely, HNCA score, NOE scores, typing and assignment probabilities that currently loaded in memory. The scroll bar at the bottom allows user to move along protein sequence.&nbsp; <br></div><div>&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>&nbsp;&nbsp;&nbsp; <br>&nbsp;&nbsp;&nbsp;&nbsp; <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp; <del style="font-weight: bold; text-decoration: none;">[[Image:Fmcgui_2.24a.jpg|thumb|left|500px]]</del></div><div>In order to modify the assignment user have first to select protein sequence segment of interest by clicking on IDs of two residues that correspond to the edges of the segment. The colour of these residues, for example K56 and D59, will change to red (see Figure 2).&nbsp;Then pressing on “Select Segment” bar at the bottom of AG window will result in possible assignment for the selected window to be shown on top-right corner of AG window.&nbsp;The possible assignments for the selected sequence segment are taken form the selected directory shown on the title bar and correspond to sub-optimal fragment assignments sampled during SA or REM calculations.</div><div>&nbsp;</div><div>&nbsp;</div> </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><div>New “Assignments Graphs” (AG) window pops up (see Figure 1). This window provides user with graphical means to manipulate&nbsp;PB fragment’s assignments without making changes of assignment status of PB fragments in memory. The current fragment’s assignment, taken from the memory, altogether with different scores associated with this assignment is shown when AG window is opened. The fragments that currently are not assigned are also shown in the bottom-right part of the AG window. User can modify the current assignment and to observe the resulting changes in the scores. </div><div>&nbsp;A particular fragment’s assignment is displayed on the left part of the AG window. The graph at the bottom shows ID of fragments assigned to each sequence position, while four graphs on the top show different scores that correspond to this assignment, namely, HNCA score, NOE scores, typing and assignment probabilities that currently loaded in memory. The scroll bar at the bottom allows user to move along protein sequence.&nbsp; <br></div><div>&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>&nbsp;&nbsp;&nbsp; <br>&nbsp;&nbsp;&nbsp;&nbsp;<ins style="font-weight: bold; text-decoration: none;">&nbsp;&nbsp;&nbsp; <br></div><div></ins><br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp; <ins style="font-weight: bold; text-decoration: none;"><br></ins></div><div>In order to modify the assignment user have first to select protein sequence segment of interest by clicking on IDs of two residues that correspond to the edges of the segment. The colour of these residues, for example K56 and D59, will change to red (see Figure 2).&nbsp;Then pressing on “Select Segment” bar at the bottom of AG window will result in possible assignment for the selected window to be shown on top-right corner of AG window.&nbsp;The possible assignments for the selected sequence segment are taken form the selected directory shown on the title bar and correspond to sub-optimal fragment assignments sampled during SA or REM calculations.</div><div>&nbsp;</div><div>&nbsp;</div> </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&nbsp;&nbsp; <br> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&nbsp;&nbsp; <br> </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"><br> </ins></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><div>The new assignment for the sequence segment should be selected from the list of possible assignments using mouse. The color of the selected line will turn red (see Figure 2.23). In the case user want to consider an assignment that is not present in the list, he should select any assignment from the list ant modify it by pressing the button “Edit” at the bottom of the AG window. A new window “Edit Assignment” pops up, and user can modify the assignment by typing changes in this window see Figure 3). </div><div>&nbsp; &nbsp; <br></div><div>[[Image:<del style="font-weight: bold; text-decoration: none;">Fmcgui_fig2</del>.24.jpg|thumb|right|250px]]</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;<br> </div> <div>Once a new assignment for the sequence segment is selected the current fragments assignment shown on the left part of AG window can be modified by pressing button “Update” &nbsp;(see Figure 2.25)</div><div>&nbsp;</div></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><div>The new assignment for the sequence segment should be selected from the list of possible assignments using mouse. The color of the selected line will turn red (see Figure 2.23). In the case user want to consider an assignment that is not present in the list, he should select any assignment from the list ant modify it by pressing the button “Edit” at the bottom of the AG window. A new window “Edit Assignment” pops up, and user can modify the assignment by typing changes in this window see Figure 3). </div><div>&nbsp; &nbsp; <br></div><div>[[Image:<ins style="font-weight: bold; text-decoration: none;">Fmcgui fig2</ins>.24.jpg|thumb|right|250px]]</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;<br> </div> <div>Once a new assignment for the sequence segment is selected the current fragments assignment shown on the left part of AG window can be modified by pressing button “Update” &nbsp;(see Figure 2.25)</div><div>&nbsp;</div> </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/div&gt;</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/div&gt;</div></td></tr>
</table>AlexLemakhttps://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/FMCGUI_commands&diff=2841&oldid=prevAlexLemak at 18:16, 2 December 20092009-12-02T18:16:00Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
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<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 18:16, 2 December 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l293">Line 293:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''View&gt;Assignment''' ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''View&gt;Assignment''' ===</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">&lt;div </del>''':''' <del style="font-weight: bold; text-decoration: none;">To display </del>assignment results<del style="font-weight: bold; text-decoration: none;">.&lt;/div&gt; </del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>''':'''<ins style="font-weight: bold; text-decoration: none;">: Display and analize </ins>assignment results </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><div>&nbsp;</div><div>The user is asked to select a directory were assignment probabilities were calculated<del style="font-weight: bold; text-decoration: none;"></div><div></del>(sa_run# or rem_run#). </div><div>&nbsp;</div><div>&nbsp;</div><<del style="font-weight: bold; text-decoration: none;">div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div</del>> </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><div>&nbsp;</div><div>The user is asked to select a directory were assignment probabilities were calculated (sa_run# or rem_run#). </div><div>&nbsp;</div><div>&nbsp;<ins style="font-weight: bold; text-decoration: none;">[[Image:Fmcgui_fig2.22.jpg|thumb|right|500px]]</ins></div><<ins style="font-weight: bold; text-decoration: none;">br</ins>></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><div>New “Assignments Graphs” (AG) window pops up (see <del style="font-weight: bold; text-decoration: none;">figure 2.22</del>). This window provides user with graphical means to manipulate&nbsp;PB<del style="font-weight: bold; text-decoration: none;">-</del>fragment’s assignments without making changes of assignment status of PB<del style="font-weight: bold; text-decoration: none;">-</del>fragments in memory. The current fragment’s assignment, taken from the memory, altogether with different scores associated with this assignment is shown when AG window is opened. The fragments that currently are not assigned are also shown in the bottom-right part of the AG window. User can modify the current assignment and to observe the resulting changes in the scores. </div><div>&nbsp;A particular fragment’s assignment is displayed on the left part of the AG window. The graph at the bottom shows ID of fragments assigned to each sequence position, while four graphs on the top show different scores that correspond to this assignment, namely, HNCA score, NOE scores, typing and assignment probabilities that currently loaded in memory. The scroll bar at the bottom allows user to move along protein sequence.</div><div><del style="font-weight: bold; text-decoration: none;">In order to modify the assignment user have first to select protein sequence segment of interest by clicking on IDs of two residues that correspond to the edges of the segment. The colour of these residues, for example K56 and D59, will change to red (see Figure 2.23).</del>&nbsp;<del style="font-weight: bold; text-decoration: none;">Then pressing on “Select Segment” bar at the bottom of AG window will result in possible assignment for the selected window to be shown on top-right corner of AG window.</del>&nbsp;<del style="font-weight: bold; text-decoration: none;">The possible assignments for the selected sequence segment are taken form the selected directory shown on the title bar and correspond to sub-optimal fragment assignments sampled during SA or REM calculations</del></div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;<<del style="font-weight: bold; text-decoration: none;">/div</del>><<del style="font-weight: bold; text-decoration: none;">div</del>>&nbsp;<<del style="font-weight: bold; text-decoration: none;">/div</del>><<del style="font-weight: bold; text-decoration: none;">div</del>>&nbsp;<<del style="font-weight: bold; text-decoration: none;">/div</del>><<del style="font-weight: bold; text-decoration: none;">div</del>>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;</div><div>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;</div><div>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;</div><div>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;</div><div>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div> </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><div>New “Assignments Graphs” (AG) window pops up (see <ins style="font-weight: bold; text-decoration: none;">Figure 1</ins>). This window provides user with graphical means to manipulate&nbsp;PB fragment’s assignments without making changes of assignment status of PB fragments in memory. The current fragment’s assignment, taken from the memory, altogether with different scores associated with this assignment is shown when AG window is opened. The fragments that currently are not assigned are also shown in the bottom-right part of the AG window. User can modify the current assignment and to observe the resulting changes in the scores. </div><div>&nbsp;A particular fragment’s assignment is displayed on the left part of the AG window. The graph at the bottom shows ID of fragments assigned to each sequence position, while four graphs on the top show different scores that correspond to this assignment, namely, HNCA score, NOE scores, typing and assignment probabilities that currently loaded in memory. The scroll bar at the bottom allows user to move along protein sequence.<ins style="font-weight: bold; text-decoration: none;">&nbsp; <br></ins></div><div>&nbsp;&nbsp;<ins style="font-weight: bold; text-decoration: none;">&nbsp;&nbsp; </ins></div><div><ins style="font-weight: bold; text-decoration: none;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</ins>&nbsp; </div><div><ins style="font-weight: bold; text-decoration: none;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</ins>&nbsp; </div><div><ins style="font-weight: bold; text-decoration: none;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</ins>&nbsp; </div><div><ins style="font-weight: bold; text-decoration: none;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</ins>&nbsp; <<ins style="font-weight: bold; text-decoration: none;">br</ins>><ins style="font-weight: bold; text-decoration: none;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </ins><<ins style="font-weight: bold; text-decoration: none;">br</ins>><ins style="font-weight: bold; text-decoration: none;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</ins>&nbsp; <<ins style="font-weight: bold; text-decoration: none;">br</ins>><ins style="font-weight: bold; text-decoration: none;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </ins><<ins style="font-weight: bold; text-decoration: none;">br</ins>><ins style="font-weight: bold; text-decoration: none;">&nbsp;&nbsp;</ins>&nbsp; <<ins style="font-weight: bold; text-decoration: none;">br</ins>><ins style="font-weight: bold; text-decoration: none;">&nbsp;&nbsp;&nbsp;&nbsp; </ins><<ins style="font-weight: bold; text-decoration: none;">br</ins>>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<ins style="font-weight: bold; text-decoration: none;">&nbsp;&nbsp;</ins>&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp; <ins style="font-weight: bold; text-decoration: none;">[[Image:Fmcgui_2.24a.jpg|thumb|left|500px]]</ins></div><div><ins style="font-weight: bold; text-decoration: none;">In order to modify the assignment user have first to select protein sequence segment of interest by clicking on IDs of two residues that correspond to the edges of the segment. The colour of these residues, for example K56 and D59, will change to red (see Figure 2).</ins>&nbsp;<ins style="font-weight: bold; text-decoration: none;">Then pressing on “Select Segment” bar at the bottom of AG window will result in possible assignment for the selected window to be shown on top-right corner of AG window.</ins>&nbsp;<ins style="font-weight: bold; text-decoration: none;">The possible assignments for the selected sequence segment are taken form the selected directory shown on the title bar and correspond to sub-optimal fragment assignments sampled during SA or REM calculations.</ins></div><div>&nbsp;</div><div>&nbsp;</div> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><br> </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">&nbsp;&nbsp; </ins><br> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><div>The new assignment for the sequence segment should be selected from the list of possible assignments using mouse. The color of the selected line will turn red (see Figure 2.23). In the case user want to consider an assignment that is not present in the list, he should select any assignment from the list ant modify it by pressing the button “Edit” at the bottom of the AG window. A new window “Edit Assignment” pops up, and user can modify the assignment by typing changes in this window see Figure <del style="font-weight: bold; text-decoration: none;">2.24</del>). <del style="font-weight: bold; text-decoration: none;">&nbsp;</del></div><div>&nbsp;</div><div><del style="font-weight: bold; text-decoration: none;">&nbsp;</del></div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div> </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"><br> </del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><div>Once a new assignment for the sequence segment is selected the current fragments assignment shown on the left part of AG window can be modified by pressing button “Update” &nbsp;(see Figure 2.25)</div><div>&nbsp;</div><del style="font-weight: bold; text-decoration: none;"><</del>/div<del style="font-weight: bold; text-decoration: none;">></del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><div>The new assignment for the sequence segment should be selected from the list of possible assignments using mouse. The color of the selected line will turn red (see Figure 2.23). In the case user want to consider an assignment that is not present in the list, he should select any assignment from the list ant modify it by pressing the button “Edit” at the bottom of the AG window. A new window “Edit Assignment” pops up, and user can modify the assignment by typing changes in this window see Figure <ins style="font-weight: bold; text-decoration: none;">3</ins>). </div><div><ins style="font-weight: bold; text-decoration: none;">&nbsp; </ins>&nbsp; <ins style="font-weight: bold; text-decoration: none;"><br></ins></div><div><ins style="font-weight: bold; text-decoration: none;">[[Image:Fmcgui_fig2.24.jpg|thumb|right|250px]]</ins></div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;<ins style="font-weight: bold; text-decoration: none;"><br> </ins></div> <div>Once a new assignment for the sequence segment is selected the current fragments assignment shown on the left part of AG window can be modified by pressing button “Update” &nbsp;(see Figure 2.25)</div><div>&nbsp;</div></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">&lt;</ins>/div<ins style="font-weight: bold; text-decoration: none;">&gt;</ins></div></td></tr>
</table>AlexLemakhttps://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/FMCGUI_commands&diff=2840&oldid=prevAlexLemak at 18:00, 2 December 20092009-12-02T18:00:21Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 18:00, 2 December 2009</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>This section provides means to visualize data and calculation results.</div><div>&nbsp;</div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>This section provides means to visualize data and calculation results.</div><div>&nbsp;</div> </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''View&gt;Fragment''' ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''View&gt;Fragment''' ===</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><div>&nbsp;''':''': Display current properties of selected fragment<br></div><div>&nbsp;</div><div>&nbsp;This command opens “Fragment Graph” (FG) &nbsp;window were all properties of a selected fragment that currently are loaded in memory will be displayed (see Figure). </div><div>&nbsp;[[Image:Fmcgui 2.21.jpg|thumb|left|550px]]</div><div>The chemical shifts making up the fragment are shown in the middle part of the window.&nbsp;The heading line (for example, line “Fragment #21 rem_run1 L108” shown on Figure 2.21) shows fragment ID (#21), the name of directory that contains assignment probabilities used to assign the fragment (rem_run1) and sequence position to which the fragment is assigned (L108). &nbsp;All other fragment properties are shown in the form of graphs. Typing probabilities&nbsp;the top section of the window one can see typing probabilities <span>&nbsp;and both assignment probabilities &nbsp;and &nbsp;&nbsp;are shown on three graph on the top part of the&nbsp;FG window.&nbsp;It is also indicated the name of the directories from which the displayed assignment probabilities were loaded (for example, on the Figure, the P<sub>SA</sub> and P<sub>REM</sub> assignmet probabilities were loaded from directories&nbsp; "sa_run2" and "rem_run2", respectively).&nbsp;Two graphs on the bottom part of the FG window shows a column ( C<sup>f</sup><sub>NOE_B</sub>(''U_id'') or C<sup>f</sup><sub>NOE_F</sub>(''U_id'') )&nbsp;and a row (C<sup>''U_id''</sup><sub>NOE_B</sub>(f) or&nbsp; </span><span>C<sup>''U_id''</sup><sub>NOE_F</sub>(f) </span><span> )&nbsp;of contact map calculated from NOESY data, respectively. Here ''U_id'' is selected fragment ID, while ''f'' is any fragment ID for which the corresponding score is &gt; 0.&nbsp;What contact map, C<sub>NOE_B</sub> or&nbsp; C<sub>NOE_F</sub>,&nbsp;is shown on the graphs is indicated on the bar at the bottom of FG window.&nbsp;Clicking on this bar using mouse will switch from one contact map to another.</span></div><div>The contact map&nbsp; <span>C<sub>HNCA</sub> is shown on this graph implicitly as well by a color of&nbsp;graph bars.</span></div><div>&nbsp;For example, on the Figure&nbsp; the elements of contact map <span>C<sub>NOE_F</sub></span> <span>related to the fragment 21 are shown. Scores for the fragment 21 to be before the fragments 37, 20 and 17 in the protein sequence &nbsp;are shown in magenta, which means that these connections being derived from NOESY data are supported by HNCA spectra as well. <del style="font-weight: bold; text-decoration: none;">Atthe </del>same&nbsp; time, scores for the fragment 21 to be before the fragments 22 and 4 are shown in red meaning that theses connections&nbsp;are not supported by HNCA&nbsp;spectra.</span></div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br></div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<br></div></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><div>&nbsp;''':''': Display current properties of selected fragment<br></div><div>&nbsp;</div><div>&nbsp;This command opens “Fragment Graph” (FG) &nbsp;window were all properties of a selected fragment that currently are loaded in memory will be displayed (see Figure). </div><div>&nbsp;[[Image:Fmcgui 2.21.jpg|thumb|left|550px]]</div><div>The chemical shifts making up the fragment are shown in the middle part of the window.&nbsp;The heading line (for example, line “Fragment #21 rem_run1 L108” shown on Figure 2.21) shows fragment ID (#21), the name of directory that contains assignment probabilities used to assign the fragment (rem_run1) and sequence position to which the fragment is assigned (L108). &nbsp;All other fragment properties are shown in the form of graphs. Typing probabilities&nbsp;the top section of the window one can see typing probabilities <span>&nbsp;and both assignment probabilities &nbsp;and &nbsp;&nbsp;are shown on three graph on the top part of the&nbsp;FG window.&nbsp;It is also indicated the name of the directories from which the displayed assignment probabilities were loaded (for example, on the Figure, the P<sub>SA</sub> and P<sub>REM</sub> assignmet probabilities were loaded from directories&nbsp; "sa_run2" and "rem_run2", respectively).&nbsp;Two graphs on the bottom part of the FG window shows a column ( C<sup>f</sup><sub>NOE_B</sub>(''U_id'') or C<sup>f</sup><sub>NOE_F</sub>(''U_id'') )&nbsp;and a row (C<sup>''U_id''</sup><sub>NOE_B</sub>(f) or&nbsp; </span><span>C<sup>''U_id''</sup><sub>NOE_F</sub>(f) </span><span> )&nbsp;of contact map calculated from NOESY data, respectively. Here ''U_id'' is selected fragment ID, while ''f'' is any fragment ID for which the corresponding score is &gt; 0.&nbsp;What contact map, C<sub>NOE_B</sub> or&nbsp; C<sub>NOE_F</sub>,&nbsp;is shown on the graphs is indicated on the bar at the bottom of FG window.&nbsp;Clicking on this bar using mouse will switch from one contact map to another.</span></div><div>The contact map&nbsp; <span>C<sub>HNCA</sub> is shown on this graph implicitly as well by a color of&nbsp;graph bars.</span></div><div>&nbsp;For example, on the Figure&nbsp; the elements of contact map <span>C<sub>NOE_F</sub></span> <span>related to the fragment 21 are shown. Scores for the fragment 21 to be before the fragments 37, 20 and 17 in the protein sequence &nbsp;are shown in magenta, which means that these connections being derived from NOESY data are supported by HNCA spectra as well. <ins style="font-weight: bold; text-decoration: none;">At the </ins>same&nbsp; time, scores for the fragment 21 to be before the fragments 22 and 4 are shown in red meaning that theses connections&nbsp;are not supported by HNCA&nbsp;spectra.</span></div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br></div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<br></div></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''View&gt;Assignment''' ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''View&gt;Assignment''' ===</div></td></tr>
</table>AlexLemakhttps://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/FMCGUI_commands&diff=2839&oldid=prevAlexLemak at 17:57, 2 December 20092009-12-02T17:57:58Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:57, 2 December 2009</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>This section provides means to visualize data and calculation results.</div><div>&nbsp;</div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>This section provides means to visualize data and calculation results.</div><div>&nbsp;</div> </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''View&gt;Fragment''' ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''View&gt;Fragment''' ===</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><div>&nbsp;''':''': Display current properties of selected fragment<br></div><div>&nbsp;</div><div>&nbsp;This command opens “Fragment Graph” (FG) &nbsp;window were all properties of a selected fragment that currently are loaded in memory will be displayed (see Figure). </div><div>&nbsp;[[Image:<del style="font-weight: bold; text-decoration: none;">Fmcgui_2</del>.21.jpg|thumb|left|550px]]</div><div>The chemical shifts making up the fragment are shown in the middle part of the window.&nbsp;The heading line (for example, line “Fragment #21 rem_run1 L108” shown on Figure 2.21) shows fragment ID (#21), the name of directory that contains assignment probabilities used to assign the fragment (rem_run1) and sequence position to which the fragment is assigned (L108). &nbsp;All other fragment properties are shown in the form of graphs. Typing probabilities&nbsp;the top section of the window one can see typing probabilities <span>&nbsp;and both assignment probabilities &nbsp;and &nbsp;&nbsp;are shown on three graph on the top part of the&nbsp;FG window.&nbsp;It is also indicated the name of the directories from which the displayed assignment probabilities were loaded.&nbsp;Two graphs on the bottom part of the FG window shows a column ( or<del style="font-weight: bold; text-decoration: none;">&nbsp;</del>)&nbsp;and a row ( or&nbsp;)&nbsp;of <del style="font-weight: bold; text-decoration: none;">a </del>contact map calculated from NOESY data, respectively. Here ''U_id'' is selected fragment ID, while ''f'' is any fragment ID for which the corresponding score is &gt; 0.&nbsp;What contact map, or <del style="font-weight: bold; text-decoration: none;">)</del>,&nbsp;is shown on the graphs is indicated on the bar at the bottom of FG window.&nbsp;Clicking on this bar <del style="font-weight: bold; text-decoration: none;">by </del>mouse will switch from one contact map to another.</span></div><div>The contact map <span><del style="font-weight: bold; text-decoration: none;">&nbsp;</del>is shown on this graph implicitly as well by color of&nbsp;graph bars.</span></div><div>&nbsp;For example, on the Figure&nbsp; the elements of contact map <span>related to the fragment 21 are shown. <del style="font-weight: bold; text-decoration: none;">The score </del>for fragment 21 to be before the fragments 37, 20 and 17 in protein sequence &nbsp;are shown in magenta which means that these connections being derived from NOESY data are supported by HNCA spectra as well. <del style="font-weight: bold; text-decoration: none;">The score </del>for fragment 21 to be before the fragments 22 and 4 are shown in red meaning that theses connections&nbsp;are not supported by HNCA&nbsp;spectra.</span></div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br></div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <<del style="font-weight: bold; text-decoration: none;">/div</del>><del style="font-weight: bold; text-decoration: none;"><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;</div><div>&nbsp;</del></div<del style="font-weight: bold; text-decoration: none;">> </del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><div>&nbsp;''':''': Display current properties of selected fragment<br></div><div>&nbsp;</div><div>&nbsp;This command opens “Fragment Graph” (FG) &nbsp;window were all properties of a selected fragment that currently are loaded in memory will be displayed (see Figure). </div><div>&nbsp;[[Image:<ins style="font-weight: bold; text-decoration: none;">Fmcgui 2</ins>.21.jpg|thumb|left|550px]]</div><div>The chemical shifts making up the fragment are shown in the middle part of the window.&nbsp;The heading line (for example, line “Fragment #21 rem_run1 L108” shown on Figure 2.21) shows fragment ID (#21), the name of directory that contains assignment probabilities used to assign the fragment (rem_run1) and sequence position to which the fragment is assigned (L108). &nbsp;All other fragment properties are shown in the form of graphs. Typing probabilities&nbsp;the top section of the window one can see typing probabilities <span>&nbsp;and both assignment probabilities &nbsp;and &nbsp;&nbsp;are shown on three graph on the top part of the&nbsp;FG window.&nbsp;It is also indicated the name of the directories from which the displayed assignment probabilities were loaded <ins style="font-weight: bold; text-decoration: none;">(for example, on the Figure, the P<sub>SA</sub> and P<sub>REM</sub> assignmet probabilities were loaded from directories&nbsp; "sa_run2" and "rem_run2", respectively)</ins>.&nbsp;Two graphs on the bottom part of the FG window shows a column ( <ins style="font-weight: bold; text-decoration: none;">C<sup>f</sup><sub>NOE_B</sub>(''U_id'') </ins>or <ins style="font-weight: bold; text-decoration: none;">C<sup>f</sup><sub>NOE_F</sub>(''U_id'') </ins>)&nbsp;and a row (<ins style="font-weight: bold; text-decoration: none;">C<sup>''U_id''</sup><sub>NOE_B</sub>(f) </ins>or&nbsp; <ins style="font-weight: bold; text-decoration: none;"></span><span>C<sup>''U_id''</sup><sub>NOE_F</sub>(f) </span><span> </ins>)&nbsp;of contact map calculated from NOESY data, respectively. Here ''U_id'' is selected fragment ID, while ''f'' is any fragment ID for which the corresponding score is &gt; 0.&nbsp;What contact map, <ins style="font-weight: bold; text-decoration: none;">C<sub>NOE_B</sub> </ins>or<ins style="font-weight: bold; text-decoration: none;">&nbsp; C<sub>NOE_F</sub></ins>,&nbsp;is shown on the graphs is indicated on the bar at the bottom of FG window.&nbsp;Clicking on this bar <ins style="font-weight: bold; text-decoration: none;">using </ins>mouse will switch from one contact map to another.</span></div><div>The contact map<ins style="font-weight: bold; text-decoration: none;">&nbsp; </ins><span><ins style="font-weight: bold; text-decoration: none;">C<sub>HNCA</sub> </ins>is shown on this graph implicitly as well by <ins style="font-weight: bold; text-decoration: none;">a </ins>color of&nbsp;graph bars.</span></div><div>&nbsp;For example, on the Figure&nbsp; the elements of contact map <ins style="font-weight: bold; text-decoration: none;"><span>C<sub>NOE_F</sub></span> </ins><span>related to the fragment 21 are shown. <ins style="font-weight: bold; text-decoration: none;">Scores </ins>for <ins style="font-weight: bold; text-decoration: none;">the </ins>fragment 21 to be before the fragments 37, 20 and 17 in <ins style="font-weight: bold; text-decoration: none;">the </ins>protein sequence &nbsp;are shown in magenta<ins style="font-weight: bold; text-decoration: none;">, </ins>which means that these connections being derived from NOESY data are supported by HNCA spectra as well. <ins style="font-weight: bold; text-decoration: none;">Atthe same&nbsp; time, scores </ins>for <ins style="font-weight: bold; text-decoration: none;">the </ins>fragment 21 to be before the fragments 22 and 4 are shown in red meaning that theses connections&nbsp;are not supported by HNCA&nbsp;spectra.</span></div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br></div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<<ins style="font-weight: bold; text-decoration: none;">br</ins>></div></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"><br</del>></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''View&gt;Assignment''' ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''View&gt;Assignment''' ===</div></td></tr>
</table>AlexLemakhttps://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/FMCGUI_commands&diff=2837&oldid=prevAlexLemak at 17:43, 2 December 20092009-12-02T17:43:02Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:43, 2 December 2009</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>This section provides means to visualize data and calculation results.</div><div>&nbsp;</div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>This section provides means to visualize data and calculation results.</div><div>&nbsp;</div> </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''View&gt;Fragment''' ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''View&gt;Fragment''' ===</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><div>&nbsp;''':''' <del style="font-weight: bold; text-decoration: none;">To display </del>current fragment <del style="font-weight: bold; text-decoration: none;">properties.</del></div><div>&nbsp;</div><div>&nbsp;This command opens “Fragment Graph” (FG) &nbsp;window were all properties of a selected fragment that currently are loaded in memory will be displayed (see Figure <del style="font-weight: bold; text-decoration: none;">2.21</del>). </div><div>&nbsp;</div><div>The chemical shifts making up the fragment are shown in the middle part of the window.&nbsp;The heading line (for example, line “Fragment #21 rem_run1 L108” shown on Figure 2.21) shows fragment ID (#21), the name of directory that contains assignment probabilities used to assign the fragment (rem_run1) and sequence position to which the fragment is assigned (L108). &nbsp;All other fragment properties are shown in the form of graphs. Typing probabilities&nbsp;the top section of the window one can see typing probabilities <span>&nbsp;and both assignment probabilities &nbsp;and &nbsp;&nbsp;are shown on three graph on the top part of the&nbsp;FG window.&nbsp;It is also indicated the name of the directories from which the displayed assignment probabilities were loaded.&nbsp;Two graphs on the bottom part of the FG window shows a column ( or&nbsp;)&nbsp;and a row ( or&nbsp;)&nbsp;of a contact map calculated from NOESY data, respectively. Here ''U_id'' is selected fragment ID, while ''f'' is any fragment ID for which the corresponding score is &gt; 0.&nbsp;What contact map, or ),&nbsp;is shown on the graphs is indicated on the bar at the bottom of FG window.&nbsp;Clicking on this bar by mouse will switch from one contact map to another.</span></div><div>The contact map <span>&nbsp;is shown on this graph implicitly as well by color of&nbsp;graph bars.</span></div><div>&nbsp;For example, on the Figure <del style="font-weight: bold; text-decoration: none;">2.21 </del>the elements of contact map <span>related to the fragment 21 are shown. The score for fragment 21 to be before the fragments 37, 20 and 17 in protein sequence &nbsp;are shown in magenta which means that these connections being derived from NOESY data are supported by HNCA spectra as well. The score for fragment 21 to be before the fragments 22 and 4 are shown in red meaning that theses connections&nbsp;are not supported by HNCA&nbsp;spectra.</span></div><div>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<<del style="font-weight: bold; text-decoration: none;">/div</del>><del style="font-weight: bold; text-decoration: none;"><div>&nbsp;</del></div><div>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;</div><div>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;</div><div>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;<del style="font-weight: bold; text-decoration: none;"></div><div></del>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div> </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><div>&nbsp;''':'''<ins style="font-weight: bold; text-decoration: none;">: Display </ins>current <ins style="font-weight: bold; text-decoration: none;">properties of selected </ins>fragment<ins style="font-weight: bold; text-decoration: none;"><br></ins></div><div>&nbsp;</div><div>&nbsp;This command opens “Fragment Graph” (FG) &nbsp;window were all properties of a selected fragment that currently are loaded in memory will be displayed (see Figure). </div><div>&nbsp;<ins style="font-weight: bold; text-decoration: none;">[[Image:Fmcgui_2.21.jpg|thumb|left|550px]]</ins></div><div>The chemical shifts making up the fragment are shown in the middle part of the window.&nbsp;The heading line (for example, line “Fragment #21 rem_run1 L108” shown on Figure 2.21) shows fragment ID (#21), the name of directory that contains assignment probabilities used to assign the fragment (rem_run1) and sequence position to which the fragment is assigned (L108). &nbsp;All other fragment properties are shown in the form of graphs. Typing probabilities&nbsp;the top section of the window one can see typing probabilities <span>&nbsp;and both assignment probabilities &nbsp;and &nbsp;&nbsp;are shown on three graph on the top part of the&nbsp;FG window.&nbsp;It is also indicated the name of the directories from which the displayed assignment probabilities were loaded.&nbsp;Two graphs on the bottom part of the FG window shows a column ( or&nbsp;)&nbsp;and a row ( or&nbsp;)&nbsp;of a contact map calculated from NOESY data, respectively. Here ''U_id'' is selected fragment ID, while ''f'' is any fragment ID for which the corresponding score is &gt; 0.&nbsp;What contact map, or ),&nbsp;is shown on the graphs is indicated on the bar at the bottom of FG window.&nbsp;Clicking on this bar by mouse will switch from one contact map to another.</span></div><div>The contact map <span>&nbsp;is shown on this graph implicitly as well by color of&nbsp;graph bars.</span></div><div>&nbsp;For example, on the Figure<ins style="font-weight: bold; text-decoration: none;">&nbsp; </ins>the elements of contact map <span>related to the fragment 21 are shown. The score for fragment 21 to be before the fragments 37, 20 and 17 in protein sequence &nbsp;are shown in magenta which means that these connections being derived from NOESY data are supported by HNCA spectra as well. The score for fragment 21 to be before the fragments 22 and 4 are shown in red meaning that theses connections&nbsp;are not supported by HNCA&nbsp;spectra.</span></div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <<ins style="font-weight: bold; text-decoration: none;">br</ins>></div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;</div><div>&nbsp;</div> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><br> </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''View&gt;Assignment''' ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''View&gt;Assignment''' ===</div></td></tr>
</table>AlexLemakhttps://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/FMCGUI_commands&diff=2834&oldid=prevAlexLemak at 17:38, 2 December 20092009-12-02T17:38:54Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<tr class="diff-title" lang="en">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:38, 2 December 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l284">Line 284:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&nbsp;''':''':&nbsp; Calculate Random Coil Index </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&nbsp;''':''':&nbsp; Calculate Random Coil Index </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><div>&nbsp;</div><div>&nbsp;</div><div>Random Coil Index &nbsp;is calculated using rci_v_1c.py script. New directory&nbsp; "rci" that contains <del style="font-weight: bold; text-decoration: none;">the </del>results of calculations is created </div><div>inside project root directory.</div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp; </div></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><div>&nbsp;</div><div>&nbsp;</div><div>Random Coil Index &nbsp;is calculated using rci_v_1c.py script. New directory&nbsp; "rci"<ins style="font-weight: bold; text-decoration: none;">, </ins>that contains results of <ins style="font-weight: bold; text-decoration: none;">the </ins>calculations<ins style="font-weight: bold; text-decoration: none;">, </ins>is created </div><div>inside project root directory.</div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div>&nbsp;&nbsp;&nbsp;&nbsp;</div></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== View menu ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== View menu ==</div></td></tr>
</table>AlexLemak