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Resonance Assignment/Abacus/Sequence specific assignment of PB fragments - Revision history
2026-04-13T17:20:38Z
Revision history for this page on the wiki
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Agutmana: moved Sequence specific assignment of PB fragments to Resonance Assignment/Abacus/Sequence specific assignment of PB fragments
2010-01-05T23:48:39Z
<p>moved <a href="/index.php/Sequence_specific_assignment_of_PB_fragments" class="mw-redirect" title="Sequence specific assignment of PB fragments">Sequence specific assignment of PB fragments</a> to <a href="/index.php/Resonance_Assignment/Abacus/Sequence_specific_assignment_of_PB_fragments" title="Resonance Assignment/Abacus/Sequence specific assignment of PB fragments">Resonance Assignment/Abacus/Sequence specific assignment of PB fragments</a></p>
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Agutmana
https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/Sequence_specific_assignment_of_PB_fragments&diff=2913&oldid=prev
AlexLemak at 23:09, 2 December 2009
2009-12-02T23:09:10Z
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:09, 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>=== Step 5. Final resonance 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>=== Step 5. Final resonance assignment ===</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>When sequence specific PB fragment assignment is done you have to put in order assigned fragments and to assign CO resonances using command { [[<del style="font-weight: bold; text-decoration: none;">FMCGUI_commands</del>#Fragment.<del style="font-weight: bold; text-decoration: none;">3EModify_Assigned</del>|Fragment&gt;Modify assigned]] }.</div><div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div><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;</div><div>When sequence specific PB fragment assignment is done you have to put in order assigned fragments and to assign CO resonances using command { [[<ins style="font-weight: bold; text-decoration: none;">FMCGUI commands</ins>#Fragment.<ins style="font-weight: bold; text-decoration: none;">3EModify_assigned</ins>|Fragment&gt;Modify assigned]] }.</div><div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div><br></div></div></td></tr>
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AlexLemak
https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/Sequence_specific_assignment_of_PB_fragments&diff=2912&oldid=prev
AlexLemak at 23:08, 2 December 2009
2009-12-02T23:08:24Z
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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>=== Step 5. Final resonance 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>=== Step 5. Final resonance assignment ===</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>When sequence specific PB<del style="font-weight: bold; text-decoration: none;">-</del>fragment assignment is done you have to put in order assigned fragments and to <del style="font-weight: bold; text-decoration: none;">assignCO </del>resonances using command<del style="font-weight: bold; text-decoration: none;">&nbsp;</del>[<del style="font-weight: bold; text-decoration: none;"><span></del>Fragment&gt;Modify assigned<del style="font-weight: bold; text-decoration: none;"></span></del>].</div><div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div><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;</div><div>When sequence specific PB fragment assignment is done you have to put in order assigned fragments and to <ins style="font-weight: bold; text-decoration: none;">assign CO </ins>resonances using command <ins style="font-weight: bold; text-decoration: none;">{ [</ins>[<ins style="font-weight: bold; text-decoration: none;">FMCGUI_commands#Fragment.3EModify_Assigned|</ins>Fragment&gt;Modify assigned]<ins style="font-weight: bold; text-decoration: none;">] }</ins>.</div><div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div><br></div></div></td></tr>
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AlexLemak
https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/Sequence_specific_assignment_of_PB_fragments&diff=2911&oldid=prev
AlexLemak at 23:06, 2 December 2009
2009-12-02T23:06:14Z
<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>=== Step 4. Assignment analysis ===</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>=== Step 4. Assignment analysis ===</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>In the case of poor data, only a part of the fragments get assigned unambiguously. The uncertainty in fragments assignment could be resolved manually with the help of FMCGUI command [<del style="font-weight: bold; text-decoration: none;"><span></del>View&gt;Assignment<del style="font-weight: bold; text-decoration: none;"></span></del>]. This command pops up “Assignment Graph” window that provides you with graphical tool to visualize the current assignment and to analyze sub-optimal fragment assignments <del style="font-weight: bold; text-decoration: none;">(see Figures 2.21-2.25)</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><div>&nbsp;</div><div>In the case of poor data, only a part of the fragments get assigned unambiguously. The uncertainty in fragments assignment could be resolved manually with the help of FMCGUI command <ins style="font-weight: bold; text-decoration: none;">{ </ins>[<ins style="font-weight: bold; text-decoration: none;">[FMCGUI_commands#View.3EAssignment|</ins>View&gt;Assignment]<ins style="font-weight: bold; text-decoration: none;">] }</ins>. This command pops up “Assignment Graph” window that provides you with graphical tool to visualize the current assignment and to analyze sub-optimal fragment assignments.</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> </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>=== Step 5. Final resonance 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>=== Step 5. Final resonance 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;"><div><div>&nbsp;</div><div>When sequence specific PB-fragment assignment is done you have to put in order assigned fragments and to assignCO resonances using command&nbsp;[<span>Fragment&gt;Modify assigned</span>].</div><div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div><br></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>&nbsp;</div><div>When sequence specific PB-fragment assignment is done you have to put in order assigned fragments and to assignCO resonances using command&nbsp;[<span>Fragment&gt;Modify assigned</span>].</div><div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div><br></div></div></td></tr>
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AlexLemak
https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/Sequence_specific_assignment_of_PB_fragments&diff=2910&oldid=prev
AlexLemak at 23:04, 2 December 2009
2009-12-02T23:04:00Z
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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>*<span>&nbsp;&nbsp; manual assignment { [[FMCGUI commands#Assignment.3EFix_Assignment.3EManually|Assignment&gt;Fix Assignment&gt;manually]] }. </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>&nbsp;&nbsp; manual assignment { [[FMCGUI commands#Assignment.3EFix_Assignment.3EManually|Assignment&gt;Fix Assignment&gt;manually]] }. </span></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>This command pops up ‘Fragment Property Modification’ window. You can change the assignment ID of any selected fragment using the bottom section of the window. </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 command pops up ‘Fragment Property Modification’ window. You can change the assignment ID of any selected fragment using the bottom section of the window. </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>*<span>&nbsp; assignment using probability map&nbsp; { [[FMCGUI commands#Assignment.3EFix_Assignment.3EUsing_Probability_map|Assignment&gt;Fix Assignment&gt;using probability map]] }.&nbsp;You have to select a calculation directory (sa_run# or rem_run#) that contains [[FMCGUI objects#Assignment_probabilities|assignment probability]] map, </span><span>, </span>and to specify the probability threshold . A fragments ''<del style="font-weight: bold; text-decoration: none;">k</del>'' will be assigned to position ''s'' if the condition<del style="font-weight: bold; text-decoration: none;">&nbsp;</del><span>&<del style="font-weight: bold; text-decoration: none;">nbsp;&nbsp</del>;&nbsp;is satisfied (see [[<del style="font-weight: bold; text-decoration: none;">Introduction_to_ABACUS</del>#Figure_1.4|Figure 1.4]]).</span></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>*<span>&nbsp; assignment using probability map&nbsp; { [[FMCGUI commands#Assignment.3EFix_Assignment.3EUsing_Probability_map|Assignment&gt;Fix Assignment&gt;using probability map]] }.&nbsp;You have to select a calculation directory (sa_run# or rem_run#) that contains [[FMCGUI objects#Assignment_probabilities|assignment probability]] map, <ins style="font-weight: bold; text-decoration: none;">P<sub>SA</sub> or P<sub>REM</sub> </ins></span><span>, </span>and to specify the probability threshold<ins style="font-weight: bold; text-decoration: none;">&nbsp; P<sub>min</sub></ins>. A fragments ''<ins style="font-weight: bold; text-decoration: none;">f</ins>'' will be assigned to position ''s'' if the condition <span><ins style="font-weight: bold; text-decoration: none;">P<sup>s</sup>(f)</ins>&<ins style="font-weight: bold; text-decoration: none;">lt</ins>;<ins style="font-weight: bold; text-decoration: none;">P<sub>min</sub> </ins>&nbsp; is satisfied (see [[<ins style="font-weight: bold; text-decoration: none;">Introduction to ABACUS</ins>#Figure_1.4|Figure 1.4]]).</span></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>&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>&nbsp;</div></div></td></tr>
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AlexLemak
https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/Sequence_specific_assignment_of_PB_fragments&diff=2909&oldid=prev
AlexLemak at 23:01, 2 December 2009
2009-12-02T23:01:08Z
<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>=== <span>Step 2.&nbsp;Probabilistic assignment of PB fragments to protein sequence</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>Step 2.&nbsp;Probabilistic assignment of PB fragments to protein sequence</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></div><div>According to [[<del style="font-weight: bold; text-decoration: none;">Introduction_to_ABACUS</del>#Figure_1.3|FMC procedure]] <del style="font-weight: bold; text-decoration: none;"> </del>you have to do the following:</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></div><div>According to [[<ins style="font-weight: bold; text-decoration: none;">Introduction to ABACUS</ins>#Figure_1.3|FMC procedure]] you have to do the following:</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>#<span>&nbsp;&nbsp;&nbsp; Probabilistic typing of PB<del style="font-weight: bold; text-decoration: none;">-</del>fragments</span> </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>#<span>&nbsp;&nbsp;&nbsp; Probabilistic typing of PB fragments</span> </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>&nbsp;&nbsp;&nbsp; </span>Calculate &nbsp;two fragments [[FMCGUI objects#Contact_map|contact maps]]&nbsp;C<sub>NOE&nbsp;</sub>and C<sub>HNCA . </sub>C<sub>NOE</sub> is a contact map based on 15N_ and 13C_NOESY data (it could be calculated by 2 different methods, “abacus” and “fawn”, respectively) and&nbsp;C<sub>HNCA</sub> is a map based on HNCA data. </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>&nbsp;&nbsp;&nbsp; </span>Calculate &nbsp;two fragments [[FMCGUI objects#Contact_map|contact maps]]&nbsp;C<sub>NOE&nbsp;</sub>and C<sub>HNCA . </sub>C<sub>NOE</sub> is a contact map based on 15N_ and 13C_NOESY data (it could be calculated by 2 different methods, “abacus” and “fawn”, respectively) and&nbsp;C<sub>HNCA</sub> is a map based on HNCA data. </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>&nbsp;&nbsp; </span>Calculate [[FMCGUI objects#Assignment_probabilities|assignment probabilities]] <span>by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo simulations</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>&nbsp;&nbsp; </span>Calculate [[FMCGUI objects#Assignment_probabilities|assignment probabilities]] <span>by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo simulations</span></div></td></tr>
</table>
AlexLemak
https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/Sequence_specific_assignment_of_PB_fragments&diff=2908&oldid=prev
AlexLemak at 22:58, 2 December 2009
2009-12-02T22:58:27Z
<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 22:58, 2 December 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l30">Line 30:</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>*<span>&nbsp;&nbsp; manual assignment { [[FMCGUI commands#Assignment.3EFix_Assignment.3EManually|Assignment&gt;Fix Assignment&gt;manually]] }. </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>&nbsp;&nbsp; manual assignment { [[FMCGUI commands#Assignment.3EFix_Assignment.3EManually|Assignment&gt;Fix Assignment&gt;manually]] }. </span></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>This command pops up ‘Fragment Property Modification’ window. You can change the assignment ID of any selected fragment using the bottom section of the window. </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 command pops up ‘Fragment Property Modification’ window. You can change the assignment ID of any selected fragment using the bottom section of the window. </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>*<span>&nbsp; assignment using probability map&nbsp; { [[FMCGUI commands#Assignment.3EFix_Assignment.3EUsing_Probability_map|Assignment&gt;Fix Assignment&gt;using probability map]] }.&nbsp;You have to select a calculation directory (sa_run# or rem_run#) that contains [[<del style="font-weight: bold; text-decoration: none;">FMCGUI_objects</del>#Assignment_probabilities|assignment probability]] map, </span><span>, </span>and to specify the probability threshold . A fragments ''k'' will be assigned to position ''s'' if the condition&nbsp;<span>&nbsp;&nbsp;&nbsp;is satisfied (see Figure 1.4).</span></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>*<span>&nbsp; assignment using probability map&nbsp; { [[FMCGUI commands#Assignment.3EFix_Assignment.3EUsing_Probability_map|Assignment&gt;Fix Assignment&gt;using probability map]] }.&nbsp;You have to select a calculation directory (sa_run# or rem_run#) that contains [[<ins style="font-weight: bold; text-decoration: none;">FMCGUI objects</ins>#Assignment_probabilities|assignment probability]] map, </span><span>, </span>and to specify the probability threshold . A fragments ''k'' will be assigned to position ''s'' if the condition&nbsp;<span>&nbsp;&nbsp;&nbsp;is satisfied (see <ins style="font-weight: bold; text-decoration: none;">[[Introduction_to_ABACUS#Figure_1.4|</ins>Figure 1.4<ins style="font-weight: bold; text-decoration: none;">]]</ins>).</span></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>&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>&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>
</table>
AlexLemak
https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/Sequence_specific_assignment_of_PB_fragments&diff=2907&oldid=prev
AlexLemak at 22:57, 2 December 2009
2009-12-02T22:57:39Z
<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;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 22:57, 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;"><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>=== <span>Step 2.&nbsp;Probabilistic assignment of PB fragments to protein sequence</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>Step 2.&nbsp;Probabilistic assignment of PB fragments to protein sequence</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></div><div>According to FMC procedure <del style="font-weight: bold; text-decoration: none;">(see Introduction) </del>you have to do the following:</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></div><div>According to <ins style="font-weight: bold; text-decoration: none;">[[Introduction_to_ABACUS#Figure_1.3|</ins>FMC procedure<ins style="font-weight: bold; text-decoration: none;">]] </ins>you have to do the following:</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>&nbsp;&nbsp;&nbsp; Probabilistic typing of PB-fragments</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>&nbsp;&nbsp;&nbsp; Probabilistic typing of PB-fragments</span> </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>&nbsp;&nbsp;&nbsp; </span>Calculate &nbsp;two fragments [[FMCGUI objects#Contact_map|contact maps]]&nbsp;C<sub>NOE&nbsp;</sub>and C<sub>HNCA . </sub>C<sub>NOE</sub> is a contact map based on 15N_ and 13C_NOESY data (it could be calculated by 2 different methods, “abacus” and “fawn”, respectively) and&nbsp;C<sub>HNCA</sub> is a map based on HNCA data. </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>&nbsp;&nbsp;&nbsp; </span>Calculate &nbsp;two fragments [[FMCGUI objects#Contact_map|contact maps]]&nbsp;C<sub>NOE&nbsp;</sub>and C<sub>HNCA . </sub>C<sub>NOE</sub> is a contact map based on 15N_ and 13C_NOESY data (it could be calculated by 2 different methods, “abacus” and “fawn”, respectively) and&nbsp;C<sub>HNCA</sub> is a map based on HNCA data. </div></td></tr>
</table>
AlexLemak
https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/Sequence_specific_assignment_of_PB_fragments&diff=2906&oldid=prev
AlexLemak at 22:55, 2 December 2009
2009-12-02T22:55:15Z
<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<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 22:55, 2 December 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l28">Line 28:</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>=== Step 3.&nbsp;Sequence-specific assignment of PB fragments by analyzing probabilities ===</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>=== Step 3.&nbsp;Sequence-specific assignment of PB fragments by analyzing probabilities ===</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>&nbsp;</div><div><span>&nbsp;&nbsp; A fragment assignment to a sequence position using FMCGUI could be done in two ways, manually and using assignment probability map, respectively. </span></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>&nbsp;</div><div><span>&nbsp;&nbsp; A fragment assignment to a sequence position using FMCGUI could be done in two ways, manually and using assignment probability map, respectively. </span></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>*<span>&nbsp;&nbsp; manual assignment { [[<del style="font-weight: bold; text-decoration: none;">FMCGUI_commands</del>#Assignment.3EFix_Assignment.3EManually|Assignment&gt;Fix Assignment&gt;manually]] }. </span></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>*<span>&nbsp;&nbsp; manual assignment { [[<ins style="font-weight: bold; text-decoration: none;">FMCGUI commands</ins>#Assignment.3EFix_Assignment.3EManually|Assignment&gt;Fix Assignment&gt;manually]] }. </span></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>This command pops up ‘Fragment Property Modification’ window. You can change the assignment ID of any selected fragment using the bottom section of the window. </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 command pops up ‘Fragment Property Modification’ window. You can change the assignment ID of any selected fragment using the bottom section of the window. </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>*<span>&nbsp; assignment using probability map&nbsp; { [[<del style="font-weight: bold; text-decoration: none;">FMCGUI_commands</del>#Assignment.3EFix_Assignment.3EUsing_Probability_map|Assignment&gt;Fix Assignment&gt;using probability map]] }.&nbsp;You have to select a calculation directory (sa_run# or rem_run#) that contains assignment probability map, </span><span>, </span>and to specify the probability threshold . A fragments ''k'' will be assigned to position ''s'' if the condition&nbsp;<span>&nbsp;&nbsp;&nbsp;is satisfied (see Figure 1.4).</span></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>*<span>&nbsp; assignment using probability map&nbsp; { [[<ins style="font-weight: bold; text-decoration: none;">FMCGUI commands</ins>#Assignment.3EFix_Assignment.3EUsing_Probability_map|Assignment&gt;Fix Assignment&gt;using probability map]] }.&nbsp;You have to select a calculation directory (sa_run# or rem_run#) that contains <ins style="font-weight: bold; text-decoration: none;">[[FMCGUI_objects#Assignment_probabilities|</ins>assignment probability<ins style="font-weight: bold; text-decoration: none;">]] </ins>map, </span><span>, </span>and to specify the probability threshold . A fragments ''k'' will be assigned to position ''s'' if the condition&nbsp;<span>&nbsp;&nbsp;&nbsp;is satisfied (see Figure 1.4).</span></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>&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>&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>
</table>
AlexLemak
https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/Sequence_specific_assignment_of_PB_fragments&diff=2905&oldid=prev
AlexLemak at 22:53, 2 December 2009
2009-12-02T22:53:13Z
<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 22:53, 2 December 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l26">Line 26:</td>
<td colspan="2" class="diff-lineno">Line 26:</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><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Calculation of assignment probabilities could be repeated a few times using different methods and parameters. Result of each calculation is stored in a separate directory. Therefore, there could be a few different directories (for example, sa_run1, sa_run2, rem_run0, rem_run1, rem_run3… ) within PRJ2/assign/ directory that contain different assignment probability maps.</span></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><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Calculation of assignment probabilities could be repeated a few times using different methods and parameters. Result of each calculation is stored in a separate directory. Therefore, there could be a few different directories (for example, sa_run1, sa_run2, rem_run0, rem_run1, rem_run3… ) within PRJ2/assign/ directory that contain different assignment probability maps.</span></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;"><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>=== Step 3.&nbsp;Sequence-specific assignment of PB fragments by analyzing probabilities<del style="font-weight: bold; text-decoration: none;">&lt;span /&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>=== Step 3.&nbsp;Sequence-specific assignment of PB fragments by analyzing probabilities ===</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>&nbsp;</div><div><span>&nbsp;&nbsp; A fragment assignment to a sequence position using FMCGUI could be done in two ways, manually and using assignment probability map, respectively. </span></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>&nbsp;</div><div><span>&nbsp;&nbsp; A fragment assignment to a sequence position using FMCGUI could be done in two ways, manually and using assignment probability map, respectively. </span></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>*<span>&nbsp;&nbsp; manual assignment [Assignment&gt;Fix Assignment&gt;manually]. </span></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>*<span>&nbsp;&nbsp; manual assignment <ins style="font-weight: bold; text-decoration: none;">{ </ins>[<ins style="font-weight: bold; text-decoration: none;">[FMCGUI_commands#Assignment.3EFix_Assignment.3EManually|</ins>Assignment&gt;Fix Assignment&gt;manually]<ins style="font-weight: bold; text-decoration: none;">] }</ins>. </span></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>This command pops up ‘Fragment Property Modification’ window. You can change the assignment ID of any selected fragment using the bottom section of the window. </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 command pops up ‘Fragment Property Modification’ window. You can change the assignment ID of any selected fragment using the bottom section of the window. </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>*<span>&nbsp; assignment using probability map&nbsp;[Assignment&gt;Fix Assignment&gt;using probability map].&nbsp;You have to select a calculation directory (sa_run# or rem_run#) that contains assignment probability map, </span><span>, </span>and to specify the probability threshold . A fragments ''k'' will be assigned to position ''s'' if the condition&nbsp;<span>&nbsp;&nbsp;&nbsp;is satisfied (see Figure 1.4).</span></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>*<span>&nbsp; assignment using probability map&nbsp; <ins style="font-weight: bold; text-decoration: none;">{ </ins>[<ins style="font-weight: bold; text-decoration: none;">[FMCGUI_commands#Assignment.3EFix_Assignment.3EUsing_Probability_map|</ins>Assignment&gt;Fix Assignment&gt;using probability map]<ins style="font-weight: bold; text-decoration: none;">] }</ins>.&nbsp;You have to select a calculation directory (sa_run# or rem_run#) that contains assignment probability map, </span><span>, </span>and to specify the probability threshold . A fragments ''k'' will be assigned to position ''s'' if the condition&nbsp;<span>&nbsp;&nbsp;&nbsp;is satisfied (see Figure 1.4).</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>&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></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> </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>=== Step 4. Assignment analysis ===</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>=== Step 4. Assignment analysis ===</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>&nbsp;</div><div>In the case of poor data, only a part of the fragments get assigned unambiguously. The uncertainty in fragments assignment could be resolved manually with the help of FMCGUI command [<span>View&gt;Assignment</span>]. This command pops up “Assignment Graph” window that provides you with graphical tool to visualize the current assignment and to analyze sub-optimal fragment assignments (see Figures 2.21-2.25).</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>&nbsp;</div><div>In the case of poor data, only a part of the fragments get assigned unambiguously. The uncertainty in fragments assignment could be resolved manually with the help of FMCGUI command [<span>View&gt;Assignment</span>]. This command pops up “Assignment Graph” window that provides you with graphical tool to visualize the current assignment and to analyze sub-optimal fragment assignments (see Figures 2.21-2.25).</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>=== Step 5. Final resonance 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>=== Step 5. Final resonance 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;"><div><div>&nbsp;</div><div>When sequence specific PB-fragment assignment is done you have to put in order assigned fragments and to assignCO resonances using command&nbsp;[<span>Fragment&gt;Modify assigned</span>].</div><div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div><br></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>&nbsp;</div><div>When sequence specific PB-fragment assignment is done you have to put in order assigned fragments and to assignCO resonances using command&nbsp;[<span>Fragment&gt;Modify assigned</span>].</div><div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div><br></div></div></td></tr>
</table>
AlexLemak