Resonance Assignment/Abacus/Spin systems format: Difference between revisions

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</pre><div><font size="2"></font></div><div><font size="2"></font></div><div><font size="2"></font></div><div><font size="2"></font></div><div><font size="2"></font></div><div><font size="2"></font></div><div><font size="2"></font></div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</div><div>'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;'''</div><div>'''2. Assigned AA-fragments in standard format.''' </div><div>&nbsp;&nbsp;&nbsp;&nbsp; </div><div></div><div></div><div></div><div></div><div></div><div>AA-fragments should be ordered in the input file according to their assignment to </div><div>protein sequence positions. </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div></div><div>
</pre><div><font size="2"></font></div><div><font size="2"></font></div><div><font size="2"></font></div><div><font size="2"></font></div><div><font size="2"></font></div><div><font size="2"></font></div><div><font size="2"></font></div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</div><div>'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;'''</div><div>'''2. Assigned AA-fragments in standard format.''' </div><div>&nbsp;&nbsp;&nbsp;&nbsp; </div><div></div><div></div><div></div><div></div><div></div><div>AA-fragments should be ordered in the input file according to their assignment to </div><div>protein sequence positions. </div><div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </div><div></div><div>
Each fragment is described as follows
Each fragment is described as follows  
<pre>
<pre>&nbsp;11 T&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp; 174.109&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 106  
&nbsp;11 T&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp; 174.109&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 106  
&nbsp;&nbsp; 8.114&nbsp; HN&nbsp;&nbsp;&nbsp; 113.206&nbsp; N  
&nbsp;&nbsp; 8.114&nbsp; HN&nbsp;&nbsp;&nbsp; 113.206&nbsp; N  
&nbsp;&nbsp; 4.325&nbsp; HA&nbsp;&nbsp;&nbsp;&nbsp; 61.900&nbsp; CA  
&nbsp;&nbsp; 4.325&nbsp; HA&nbsp;&nbsp;&nbsp;&nbsp; 61.900&nbsp; CA  
&nbsp;&nbsp; 4.283&nbsp; HB&nbsp;&nbsp;&nbsp;&nbsp; 69.855&nbsp; CB  
&nbsp;&nbsp; 4.283&nbsp; HB&nbsp;&nbsp;&nbsp;&nbsp; 69.855&nbsp; CB  
&nbsp;&nbsp; 1.126&nbsp; HG2*&nbsp;&nbsp; 21.639&nbsp; CG2</pre>
&nbsp;&nbsp; 1.126&nbsp; HG2*&nbsp;&nbsp; 21.639&nbsp; CG2</pre>
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&nbsp;&nbsp; 0.642&nbsp; HG2*&nbsp;&nbsp; 20.806&nbsp; CG2  
&nbsp;&nbsp; 0.642&nbsp; HG2*&nbsp;&nbsp; 20.806&nbsp; CG2  
...........&nbsp;&nbsp;  
...........&nbsp;&nbsp;  
</pre><div>&nbsp;</div><div>&nbsp;</div><div><font size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</font></div><div><font size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</font></div><div><font size="2"></font></div><div><font size="2"></font></div></font>
</pre><div>&nbsp;</div><div>&nbsp;</div><div><font size="2">&nbsp;&nbsp;</font></div><div><font size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</font></div><div><font size="2"></font></div><div><font size="2"></font></div></font>
<div>'''<span id="1259349916483S" style="display: none">&nbsp;</span>3. CYANA chemical shift file (prot-file).'''</div><div></div><div></div><div>Assigned chemical shifts caould be loaded in FMCGUI and automatically transformed in a set of assigned PB-frsagments.</div><div></div><div></div><div></div><div></div><div>''<font size="2">Example</font>''<font size="2">3.1. Assigned chemical shifts.</font></div><div><font size="2"></font></div><div><font size="2"></font></div><div><font size="2"></font></div><div><font size="2"></font></div><div></div><div></div>
<div>'''<span id="1259349916483S" style="display: none">&nbsp;</span>3. CYANA chemical shift file (prot-file).'''</div><div>'''&nbsp;&nbsp;&nbsp;&nbsp;'''</div><div></div><div></div><div>Assigned chemical shifts caould be loaded in FMCGUI and automatically transformed in a set of assigned PB-frsagments.</div><div>&nbsp;&nbsp;&nbsp; </div><div></div><div></div><div></div><div></div><div></div><div>''<font size="2">Example</font>''<font size="2">3.1. Assigned chemical shifts.</font></div><div><font size="2">&nbsp;&nbsp;</font></div><pre><font size="2"> &nbsp;&nbsp;  1&nbsp;&nbsp; 8.414&nbsp;&nbsp; 0.000 H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1
&nbsp;&nbsp;&nbsp;&nbsp; 2 123.795&nbsp;&nbsp; 0.000 N&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1
&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp; 4.723&nbsp;&nbsp; 0.000 HA&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1
&nbsp;&nbsp;&nbsp;&nbsp; 4&nbsp; 53.298&nbsp;&nbsp; 0.000 CA&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1
&nbsp;&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp; 1.898&nbsp;&nbsp; 0.000 HB3&nbsp;&nbsp;&nbsp;&nbsp; 1
&nbsp;&nbsp;&nbsp;&nbsp; 6&nbsp; 32.288&nbsp;&nbsp; 0.000 CB&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1
&nbsp;&nbsp;&nbsp;&nbsp; 7&nbsp;&nbsp; 2.030&nbsp;&nbsp; 0.000 HB2&nbsp;&nbsp;&nbsp;&nbsp; 1
&nbsp;&nbsp;&nbsp;&nbsp; 8&nbsp;&nbsp; 2.475&nbsp;&nbsp; 0.000 HG3&nbsp;&nbsp;&nbsp;&nbsp; 1
&nbsp;&nbsp;&nbsp;&nbsp; 9&nbsp; 32.024&nbsp;&nbsp; 0.000 CG&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1
&nbsp;&nbsp;&nbsp; 10&nbsp;&nbsp; 2.547&nbsp;&nbsp; 0.000 HG2&nbsp;&nbsp;&nbsp;&nbsp; 1
&nbsp;&nbsp;&nbsp; 11 177.440&nbsp;&nbsp; 0.000 C&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2
&nbsp;&nbsp;&nbsp; 12&nbsp;&nbsp; 4.379&nbsp;&nbsp; 0.000 HA&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2
&nbsp;&nbsp;&nbsp; 13&nbsp; 63.455&nbsp;&nbsp; 0.000 CA&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2
&nbsp;&nbsp;&nbsp; 14&nbsp;&nbsp; 1.914&nbsp;&nbsp; 0.000 HB3&nbsp;&nbsp;&nbsp;&nbsp; 2
&nbsp;&nbsp;&nbsp; 15&nbsp; 32.194&nbsp;&nbsp; 0.000 CB&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2
&nbsp;&nbsp;&nbsp; 16&nbsp;&nbsp; 2.268&nbsp;&nbsp; 0.000 HB2&nbsp;&nbsp;&nbsp;&nbsp; 2
&nbsp;&nbsp;&nbsp; 17&nbsp;&nbsp; 1.971&nbsp;&nbsp; 0.000 HG3&nbsp;&nbsp;&nbsp;&nbsp; 2
&nbsp;&nbsp;&nbsp; 18&nbsp; 27.313&nbsp;&nbsp; 0.000 CG&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2
&nbsp;&nbsp;&nbsp; 19&nbsp;&nbsp; 2.008&nbsp;&nbsp; 0.000 HG2&nbsp;&nbsp;&nbsp;&nbsp; 2
&nbsp;&nbsp;&nbsp; 20&nbsp;&nbsp; 3.650&nbsp;&nbsp; 0.000 QD&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2
&nbsp;&nbsp;&nbsp; 21&nbsp; 50.670&nbsp;&nbsp; 0.000 CD&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2
&nbsp;&nbsp;&nbsp; 22 173.945&nbsp;&nbsp; 0.000 C&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3
&nbsp;&nbsp;&nbsp; 23&nbsp;&nbsp; 8.438&nbsp;&nbsp; 0.000 H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3
&nbsp;&nbsp;&nbsp; 24 108.915&nbsp;&nbsp; 0.000 N&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3
&nbsp;&nbsp;&nbsp; 25&nbsp;&nbsp; 3.941&nbsp;&nbsp; 0.000 QA&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3
&nbsp;&nbsp;&nbsp; 26&nbsp; 45.341&nbsp;&nbsp; 0.000 CA&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3
..................................  </font></pre><div><font size="2">&nbsp;&nbsp;</font></div><div><font size="2"></font></div><div><font size="2"></font></div><div><font size="2"></font></div><div><font size="2"></font></div><div></div><div></div>

Revision as of 20:07, 27 November 2009

Not assigned spin-systems (PB fragments) could be loaded in FMCGUI using only one, "standad", format.
Assigned chemical shifts (spin-systems) could be loaded using two different formats, standard and cyana format.
 
1. PB-fragments in standard format.
Each fragment is represented by a number of lines. The groups of lines corresponding to different fragments are separated by empty line.
The line that follow the last fragment should have 'Q' at the first position.
 
A fragment is described as follows:
31 X    7     0.000  
   9.025  HN    106.560  N 
   5.221  HA     55.302  CA 
   1.940  HB*    33.679  CB 
   1.480  HG1    27.976  CG 
   1.775  HG2    27.976  CG 
   2.943  HD1    43.958  CD 
   3.205  HD2    43.958  CD
   
Here, the first line specify user ID, 1-letter residue type ('X' if not known), the number of the following lines (regading the fragment), and chemical shift of backbone C' atom ( should be '0.000' if it is not known).
 
 The fragments user ID could be any digit number < 500. There is no restriction on the order of fragments in the input file.
 
Example1.1. Not assigned PB-fragments.
 90 X    5     0.000 

   8.462  HN    122.771  N 
   4.262  HA     56.242  CA 
   1.880  HB1    30.528  CB 
   2.006  HB2    30.528  CB 
   2.222  HG*    36.201  CG 
    
 91 S    4   174.082 
   8.089  HN    123.488  N 
   4.626  HA     55.058  CA 
   3.413  HB1    65.338  CB 
   3.801  HB2    65.338  CB 
    
247 X    5     0.000 
   8.070  HN    123.607  N 
   4.034  HA     62.358  CA 
   2.048  HB     32.775  CB 
   0.873  HG1*   21.111  CG1 
   0.884  HG2*   20.501  CG2 
    
 18 X    4     0.000 
   8.110  HN    123.044  N 
   5.042  HA     58.559  CA 
   4.179  HB     70.135  CB 
   0.087  HG2*   16.018  CG2 
Q
        
         
2. Assigned AA-fragments in standard format.
    
AA-fragments should be ordered in the input file according to their assignment to
protein sequence positions.
       

Each fragment is described as follows 

 11 T    4   174.109         106 
   8.114  HN    113.206  N 
   4.325  HA     61.900  CA 
   4.283  HB     69.855  CB 
   1.126  HG2*   21.639  CG2

 

 

Here, the first line specifies  protein sequence position to which the fragment is assigned, 1-letter amino acid type, the number of the following lines describing the fragment, chemical shift of backbone C' atom, and user ID of the fragment.The last number, user ID, is optional.
 
Example2.1. Assigned AA-fragments with user ID specified.
  
...............................
 10 G    2   174.136         158 
   8.605  HN    110.399  N 
   3.708  HA*    46.225  CA 
    
 11 T    4   174.109         106 
   8.114  HN    113.206  N 
   4.325  HA     61.900  CA 
   4.283  HB     69.855  CB 
   1.126  HG2*   21.639  CG2 
    
 12 N    1   175.100         999 
   8.231  HN    122.327  N 
    
 16 A    2   179.269          50 
   3.224  HA     56.082  CA 
   1.518  HB*    18.860  CB 
    
 17 D    3   179.378          74 
   8.451  HN    116.577  N 
   4.370  HA     57.335  CA 
   2.656  HB*    39.698  CB 
    
 18 V    5   177.276         117 
   7.579  HN    122.993  N 
   3.720  HA     65.701  CA 
   2.068  HB     31.930  CB 
   1.160  HG1*   22.719  CG1 
   0.642  HG2*   20.806  CG2 
............................  
  
 
Example2.2. Assigned AA-fragments without user ID specified.
   
.....
 10 G    2   174.136         158 
   8.605  HN    110.399  N 
   3.708  HA*    46.225  CA 
    
 11 T    4   174.109         106 
   8.114  HN    113.206  N 
   4.325  HA     61.900  CA 
   4.283  HB     69.855  CB 
   1.126  HG2*   21.639  CG2 
    
 12 N    1   175.100         999 
   8.231  HN    122.327  N 
    
 16 A    2   179.269          50 
   3.224  HA     56.082  CA 
   1.518  HB*    18.860  CB 
    
 17 D    3   179.378          74 
   8.451  HN    116.577  N 
   4.370  HA     57.335  CA 
   2.656  HB*    39.698  CB 
    
 18 V    5   177.276         117 
   7.579  HN    122.993  N 
   3.720  HA     65.701  CA 
   2.068  HB     31.930  CB 
   1.160  HG1*   22.719  CG1 
   0.642  HG2*   20.806  CG2 
...........  
 
 
  
     
3. CYANA chemical shift file (prot-file).
    
Assigned chemical shifts caould be loaded in FMCGUI and automatically transformed in a set of assigned PB-frsagments.
   
Example3.1. Assigned chemical shifts.
  
<font size="2">     1   8.414   0.000 H       1 
     2 123.795   0.000 N       1 
     3   4.723   0.000 HA      1 
     4  53.298   0.000 CA      1 
     5   1.898   0.000 HB3     1 
     6  32.288   0.000 CB      1 
     7   2.030   0.000 HB2     1 
     8   2.475   0.000 HG3     1 
     9  32.024   0.000 CG      1 
    10   2.547   0.000 HG2     1 
    11 177.440   0.000 C       2 
    12   4.379   0.000 HA      2 
    13  63.455   0.000 CA      2 
    14   1.914   0.000 HB3     2 
    15  32.194   0.000 CB      2 
    16   2.268   0.000 HB2     2 
    17   1.971   0.000 HG3     2 
    18  27.313   0.000 CG      2 
    19   2.008   0.000 HG2     2 
    20   3.650   0.000 QD      2 
    21  50.670   0.000 CD      2 
    22 173.945   0.000 C       3 
    23   8.438   0.000 H       3 
    24 108.915   0.000 N       3 
    25   3.941   0.000 QA      3 
    26  45.341   0.000 CA      3 
..................................  </font>
  
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