Resonance Assignment/Abacus/FMCGUI commands: Difference between revisions

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2. Project Menu  
== 2. Project Menu ==


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<div><span>['''Project&gt;New''']:&nbsp;To start a new project. </span></div><div>&nbsp;</div><div>User have to provide a name of the project PROJECTNAME,and to select a directory that will host the project. The project root directory with the same name&nbsp;PROJECTNAME is created. </div><div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div>['''<span>Project&gt;Load</span>''']: To continue to work on previously saved project.</div><div>&nbsp;</div><div>User have to select file PROJECTNAME.prj in the directory PROJECTNAME, where PROJECTNAME is the name of the root directory of the project.</div><div>&nbsp;</div><div>['''<span>Project&gt;Save</span>'''] : To 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>
['''<span>Poject&gt;Quit</span>'''] : To save the current state of the project and to quit.


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=== <span>'''Project&gt;New'''</span> ===
<div><span>:Start a new project. </span></div><div><span /></div><div>&nbsp;User have to provide a name of the project PROJECTNAME,and to select a directory that will host the project. The project root directory with the same name&nbsp;PROJECTNAME is created. </div><div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div>
=== '''<span>Project&gt;Load</span>''' ===
<div>: Continue to work on previously saved project.</div><div>&nbsp;</div><div>User have to select file PROJECTNAME.prj in the directory PROJECTNAME, where PROJECTNAME is the name of the root directory of the project.</div><div>&nbsp;</div>
=== '''<span>Project&gt;Save</span>''' ===
<div></div><div>&nbsp;: To 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>
=== '''<span>Poject&gt;Quit</span>'''&nbsp; ===


3. Data Menu
: To save the current state of the project and to quit.  


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&nbsp;  


== 3. Data Menu  ==


<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>['''<span>Data&gt;Protein Sequence&gt;Load</span>'''] : To load a protein sequence into memory.</div><div>&nbsp;</div><div>&nbsp;</div><div>''The input formats'': </div><div><span>&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; 1-letter code (fasta format); </span></div><div><span>&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;3-letter code (standard format).</span></div><div>&nbsp;</div><div>User have to select the file with sequence and to specify the first residue ID in case it is not specified in the input file. </div><div>If there is His-tag in the sequence file, it is recommended&nbsp;to set&nbsp;the first residue ID&nbsp; to a negative number such that the first&nbsp;residue of a protein has ID of 1. </div><div>&nbsp;</div><div>['''<span>Data&gt;Protein Sequence&gt;Save as</span>'''] : To save protein sequence in the file on disk.</div><div>&nbsp;</div><div>''The output formats'':</div><div><span>&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;1-letter code (fasta format);</span></div><div><span>&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;3-letter code ("standard" format, for cyana)</span></div><div><span>&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;3-letter code (for AutoStructure);</span></div><div><span>&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;3-letter code (for RCI);</span></div><div>&nbsp;</div><div>There are separate buttons for different peak lists. </div><div>&nbsp;</div><div>['''<span>Data&gt;N15 NOESY&gt;load/Save as</span>''']</div><div>['''<span>Data&gt;C13 NOESY&gt;load/Save as</span>''']</div><div>['''<span>Data&gt;Arom NOESY&gt;load/Save as</span>''']</div><div>['''<span>Data&gt;N15 HSQC&gt;load/Save as</span>''']</div><div>['''<span>Data&gt;C13 HSQC&gt;load/Save as</span>''']</div><div>['''<span>Data&gt;HNCA&gt;load/Save as</span>''']</div><div>['''<span>Data&gt;HNCO&gt;load/Save as</span>''']</div><div>['''<span>Data&gt;CBCACONHN&gt;load/Save as</span>''']</div><div>['''<span>Data&gt;HBHACONH&gt;load/Save as</span>''']&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; :&nbsp;&nbsp; To load or save a peak list.</div><div>&nbsp;</div><div>''Input and output formats'':&nbsp;</div><div><span>&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; - Sparky;</span></div><div><span>&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; -&nbsp;Xeasy;</span></div><div><span>&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; -&nbsp;Standard;</span></div><div><span>&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; </span></div><div>['''<span>Data&gt;Tolerances</span>'''] : To set tolerances for chemical shift matching in different spectral dimensions.</div><div>&nbsp;</div>
&nbsp;
 
<br>
<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>
=== '''<span>Data&gt;Protein Sequence&gt;Load</span>'''&nbsp; ===
<div></div><div>: To load a protein sequence into memory.</div><div>&nbsp;</div><div>&nbsp;</div><div>''The input formats'': </div><div><span>&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; 1-letter code (fasta format); </span></div><div><span>&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;3-letter code (standard format).</span></div><div>&nbsp;</div><div>User have to select the file with sequence and to specify the first residue ID in case it is not specified in the input file. </div><div>If there is His-tag in the sequence file, it is recommended&nbsp;to set&nbsp;the first residue ID&nbsp; to a negative number such that the first&nbsp;residue of a protein has ID of 1. </div><div>&nbsp;</div>
=== '''<span>Data&gt;Protein Sequence&gt;Save as</span>''' ===
<div></div><div>: To save protein sequence in the file on disk.</div><div>&nbsp;</div><div>''The output formats'':</div><div><span>&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;1-letter code (fasta format);</span></div><div><span>&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;3-letter code ("standard" format, for cyana)</span></div><div><span>&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;3-letter code (for AutoStructure);</span></div><div><span>&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;3-letter code (for RCI);</span></div><div>&nbsp;</div><div>There are separate buttons for different peak lists. </div><div>&nbsp;</div>
=== '''<span>Data&gt;N15 NOESY&gt;</span>''' ===
<div>'''<span />'''</div>
=== '''<span>Data&gt;C13 NOESY&gt;</span>''' ===
<div>'''<span />'''</div>
=== '''<span>Data&gt;Arom NOESY&gt;</span>''' ===
<div>'''<span />'''</div>
=== '''<span>Data&gt;N15 HSQC&gt;</span>''' ===
<div>'''<span />'''</div>
=== '''<span>Data&gt;C13 HSQC&gt;</span>''' ===
<div></div>
=== '''<span>Data&gt;HNCA&gt;</span>''' ===
<div></div>
=== '''<span>Data&gt;HNCO&gt;</span>''' ===
<div>'''<span />'''</div>
=== '''<span>Data&gt;CBCACONHN&gt;</span>''' ===
<div></div>
=== '''<span>Data&gt;HBHACONH&gt;</span>''' ===
<div>'''<span />'''</div><div>&nbsp;:&nbsp;&nbsp; Load or save a peak list.</div><div>&nbsp;</div><div>''Input and output formats'':&nbsp;</div><div><span>&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; - Sparky;</span></div><div><span>&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; -&nbsp;Xeasy;</span></div><div><span>&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; -&nbsp;Standard</span></div><div><span>&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; </span></div>
=== '''<span>Data&gt;Tolerances</span>''' ===
<div></div><div>: To set tolerances for chemical shift matching in different spectral dimensions.</div><div>&nbsp;</div>

Revision as of 23:15, 27 November 2009

 

2. Project Menu

 

Project>New

:Start a new project.
 User have to provide a name of the project PROJECTNAME,and to select a directory that will host the project. The project root directory with the same name PROJECTNAME is created.
             

Project>Load

: Continue to work on previously saved project.
 
User have to select file PROJECTNAME.prj in the directory PROJECTNAME, where PROJECTNAME is the name of the root directory of the project.
 

Project>Save

 : To save the current state of the project.
 
What is currently in the computer memory is saved in the file PROJECTNAME.prj located in the root directory of the project.
 

Poject>Quit 

To save the current state of the project and to quit.

 

3. Data Menu

 


The DATA section serves to load&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.
 

Data>Protein Sequence>Load 

: To load a protein sequence into memory.
 
 
The input formats:
                             -   1-letter code (fasta format);
                             -   3-letter code (standard format).
 
User have to select the file with sequence and to specify the first residue ID in case it is not specified in the input file.
If there is His-tag in the sequence file, it is recommended to set the first residue ID  to a negative number such that the first residue of a protein has ID of 1.
 

Data>Protein Sequence>Save as

: To save protein sequence in the file on disk.
 
The output formats:
                               - 1-letter code (fasta format);
                               -  3-letter code ("standard" format, for cyana)
                               -   3-letter code (for AutoStructure);
                               -  3-letter code (for RCI);
 
There are separate buttons for different peak lists.
 

Data>N15 NOESY>

Data>C13 NOESY>

Data>Arom NOESY>

Data>N15 HSQC>

Data>C13 HSQC>

Data>HNCA>

Data>HNCO>

Data>CBCACONHN>

Data>HBHACONH>

 :   Load or save a peak list.
 
Input and output formats: 
                                        - Sparky;
                                        - Xeasy;
                                         - Standard
                                      

Data>Tolerances

: To set tolerances for chemical shift matching in different spectral dimensions.
 
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