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

Revision as of 19:49, 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

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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.

<font size="2"> ...............................

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 ............................

</font>

Example2.2. Assigned AA-fragments without user ID specified.

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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.

@@ Line 34: / Line 34: @@
 Q
-</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</div><div</div><div>'''2. Assigned AA-fragments in standard format.''' </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></div><div>Each fragment is described as follows: </div><pre>&nbsp;11 T&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp; 174.109&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 106
+</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</div><div>'''&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: </div><pre>&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; 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; 1.126&nbsp; HG2*&nbsp;&nbsp; 21.639&nbsp; CG2 </pre><div></div><div></div><div></div><div>Here, the first line specifies&nbsp; 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.</div><div></div><div></div><div>&nbsp;</div><div>''<font size="2">Example</font>''<font size="2">2.1. Assigned AA-fragments with user ID specified.</font></div><div><font size="2"></font></div><div><font size="2"></font></div><div><font size="2"></font><div><font size="2">''<font size="2"></font>''</font></div></div>
+ &nbsp; 1.126&nbsp; HG2*&nbsp;&nbsp; 21.639&nbsp; CG2 </pre><div></div><div></div><div></div><div>Here, the first line specifies&nbsp; 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.</div><div></div><div></div><div>&nbsp;</div><div>''<font size="2">Example</font>''<font size="2">2.1. Assigned AA-fragments with user ID specified.</font></div><div><font size="2">&nbsp;&nbsp;</font></div><pre><font size="2"> ...............................
+&nbsp;10 G&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp; 174.136&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 158
+&nbsp;&nbsp; 8.605&nbsp; HN&nbsp;&nbsp;&nbsp; 110.399&nbsp; N
+&nbsp;&nbsp; 3.708&nbsp; HA*&nbsp;&nbsp;&nbsp; 46.225&nbsp; CA
+&nbsp;&nbsp;&nbsp;
+&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; 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; 1.126&nbsp; HG2*&nbsp;&nbsp; 21.639&nbsp; CG2
+&nbsp;&nbsp;&nbsp;
+&nbsp;12 N&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp; 175.100&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 999
+&nbsp;&nbsp; 8.231&nbsp; HN&nbsp;&nbsp;&nbsp; 122.327&nbsp; N
+&nbsp;&nbsp;&nbsp;
+&nbsp;16 A&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp; 179.269&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 50
+&nbsp;&nbsp; 3.224&nbsp; HA&nbsp;&nbsp;&nbsp;&nbsp; 56.082&nbsp; CA
+&nbsp;&nbsp; 1.518&nbsp; HB*&nbsp;&nbsp;&nbsp; 18.860&nbsp; CB
+&nbsp;&nbsp;&nbsp;
+&nbsp;17 D&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp; 179.378&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 74
+&nbsp;&nbsp; 8.451&nbsp; HN&nbsp;&nbsp;&nbsp; 116.577&nbsp; N
+&nbsp;&nbsp; 4.370&nbsp; HA&nbsp;&nbsp;&nbsp;&nbsp; 57.335&nbsp; CA
+&nbsp;&nbsp; 2.656&nbsp; HB*&nbsp;&nbsp;&nbsp; 39.698&nbsp; CB
+&nbsp;&nbsp;&nbsp;
+&nbsp;18 V&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp; 177.276&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 117
+&nbsp;&nbsp; 7.579&nbsp; HN&nbsp;&nbsp;&nbsp; 122.993&nbsp; N
+&nbsp;&nbsp; 3.720&nbsp; HA&nbsp;&nbsp;&nbsp;&nbsp; 65.701&nbsp; CA
+&nbsp;&nbsp; 2.068&nbsp; HB&nbsp;&nbsp;&nbsp;&nbsp; 31.930&nbsp; CB
+&nbsp;&nbsp; 1.160&nbsp; HG1*&nbsp;&nbsp; 22.719&nbsp; CG1
+&nbsp;&nbsp; 0.642&nbsp; HG2*&nbsp;&nbsp; 20.806&nbsp; CG2
+............................&nbsp;&nbsp;
+  </font></pre><div><font size="2">&nbsp;&nbsp;</font></div><div><font size="2">&nbsp;</font></div><div><font size="2"></font></div><div><font size="2"></font></div><div><font size="2"></font><div><font size="2">''<font size="2"></font>''</font></div></div>
 <font size="2"><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>''<font size="2">Example</font>''<font size="2">2.2. Assigned AA-fragments without user ID specified.</font></div><div><font size="2"></font></div><div><font size="2"></font></div></font>&lt;div&lt;/div&gt;&lt;div&lt;/div&gt;&lt;&lt;/div&gt;
 <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>

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

Revision as of 19:49, 27 November 2009

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