Resonance Assignment/Abacus/Spin systems format: Difference between revisions
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<div>Not assigned spin-systems ([[Introduction to ABACUS#PB_fragment|PB fragments]]) could be loaded in FMCGUI using only one, "standad", format.</div><div>Assigned chemical shifts (spin-systems) could be loaded using two different formats, standard and cyana format.</div><div> </div> | <div>Not assigned spin-systems ([[Introduction to ABACUS#PB_fragment|PB fragments]]) could be loaded in FMCGUI using only one, "standad", format.</div><div>Assigned chemical shifts (spin-systems) could be loaded using two different formats, standard and cyana format.</div><div> </div> | ||
=== '''1. PB-fragments in standard format.''' === | |||
__TOC__ | |||
=== '''1. PB-fragments in standard format.''' === | |||
<div></div><div></div><div></div><div>Each fragment is represented by a number of lines. The groups of lines corresponding to different fragments are separated by empty line. </div><div>The line that follow the last fragment should have 'Q' at the first position.</div><div> </div><div>A fragment is described as follows:</div><div></div><pre>31 X 7 0.000 | <div></div><div></div><div></div><div>Each fragment is represented by a number of lines. The groups of lines corresponding to different fragments are separated by empty line. </div><div>The line that follow the last fragment should have 'Q' at the first position.</div><div> </div><div>A fragment is described as follows:</div><div></div><pre>31 X 7 0.000 | ||
9.025 HN 106.560 N | 9.025 HN 106.560 N | ||
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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> </div><div>''' '''</div> | |||
=== '''2. Assigned AA-fragments in standard format.''' === | === '''2. Assigned AA-fragments in standard format.''' === | ||
<div> </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></div><div> | <div> </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></div><div> | ||
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=== '''<span | === '''<span style="display: none;" id="1259349916483S"> </span>3. CYANA chemical shift file (prot-file).''' === | ||
<div>''' '''</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></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><pre> 1 8.414 0.000 H 1 | <div>''' '''</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></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><pre> 1 8.414 0.000 H 1 | ||
2 123.795 0.000 N 1 | 2 123.795 0.000 N 1 | ||
Revision as of 17:05, 1 December 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 0.0008.462 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 8.605 HN 110.399 N 3.708 HA* 46.225 CA 11 T 4 174.109 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 8.231 HN 122.327 N 16 A 2 179.269 3.224 HA 56.082 CA 1.518 HB* 18.860 CB 17 D 3 179.378 8.451 HN 116.577 N 4.370 HA 57.335 CA 2.656 HB* 39.698 CB 18 V 5 177.276 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.
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 ..................................