Resonance Assignment/Abacus/Spin systems format
Jump to navigation
Jump to search
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.
<div</div>
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:
<font size="2">31 X<span> 7 0.000 </span></font><div><span><font size="2"> 9.025 HN 106.560 N </font></span></div><div><font size="2"><span> 5.221 HA 55.302 CA </span></font></div><div><font size="2"><span> 1.940 HB* 33.679 CB </span></font></div><div><font size="2"><span> 1.480 HG1 27.976 CG </span></font></div><div><font size="2"><span> 1.775 HG2 27.976 CG </span></font></div><div><font size="2"><span> 2.943 HD1 43.958 CD </span></font></div><div><font size="2"><span> 3.205 HD2 43.958 CD </span></font></div><div><font size="2"><span /></font></div><span><font size="2"></font></span>
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.<span /><span />
<div><font size="2"><span> 90 X 5 0.000</span></font></div><div><font size="2"><span> 8.462 HN 122.771 N </span></font></div><div><font size="2"><span> 4.262 HA 56.242 CA </span></font></div><div><font size="2"><span> 1.880 HB1 30.528 CB </span></font></div><div><font size="2"><span> 2.006 HB2 30.528 CB </span></font></div><div><font size="2"><span> 2.222 HG* 36.201 CG </span></font></div><div><span><font size="2"> </font></span></div><div><font size="2"> 91 S<span> 4 174.082 </span></font></div><div><font size="2"><span> 8.089 HN 123.488 N </span></font></div><div><font size="2"><span> 4.626 HA 55.058 CA </span></font></div><div><font size="2"><span> 3.413 HB1 65.338 CB </span></font></div><div><font size="2"><span> 3.801 HB2 65.338 CB </span></font></div><div><span><font size="2"> </font></span></div><div><font size="2">247 X<span> 5 0.000 </span></font></div><div><font size="2"><span> 8.070 HN 123.607 N </span></font></div><div><font size="2"><span> 4.034 HA 62.358 CA </span></font></div><div><font size="2"><span> 2.048 HB 32.775 CB </span></font></div><div><font size="2"><span> 0.873 HG1* 21.111 CG1 </span></font></div><div><font size="2"><span> 0.884 HG2* 20.501 CG2 </span></font></div><div><span><font size="2"> </font></span></div><div><font size="2"> 18 X<span> 4 0.000 </span></font></div><div><font size="2"><span> 8.110 HN 123.044 N </span></font></div><div><font size="2"><span> 5.042 HA 58.559 CA </span></font></div><div><font size="2"><span> 4.179 HB 70.135 CB </span></font></div><div><font size="2"><span> 0.087 HG2* 16.018 CG2 </span></font></div><div><font size="2">Q</font></div><font size="2"></font>
2. Assigned AA-fragments in standard format.
<div</div>
AA-fragments should be ordered in the input file according to their assignment to
protein sequence positions.
Each fragment is described as follows:
<font size="2">11 T<span> 4 174.109 106 </span></font><div><span><font size="2"> 8.114 HN 113.206 N </font></span></div><div><font size="2"><span> 4.325 HA 61.900 CA </span></font></div><div><font size="2"><span> 4.283 HB 69.855 CB </span></font></div><div><font size="2"><span> 1.126 HG2* 21.639 CG2 </span></font></div>
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.
<div><font size="2">.........................</font></div><div><font size="2"> 10 G<span> 2 174.136 158 </span></font></div><div><font size="2"><span> 8.605 HN 110.399 N </span></font></div><div><font size="2"><span> 3.708 HA* 46.225 CA </span></font></div><div><span><font size="2"> </font></span></div><div><font size="2"> 11 T<span> 4 174.109 106 </span></font></div><div><font size="2"><span> 8.114 HN 113.206 N </span></font></div><div><font size="2"><span> 4.325 HA 61.900 CA </span></font></div><div><font size="2"><span> 4.283 HB 69.855 CB </span></font></div><div><font size="2"><span> 1.126 HG2* 21.639 CG2 </span></font></div><div><span><font size="2"> </font></span></div><div><font size="2"> 12 N<span> 1 175.100 999 </span></font></div><div><font size="2"><span> 8.231 HN 122.327 N </span></font></div><div><span><font size="2"> </font></span></div><div><font size="2"> 16 A<span> 2 179.269 50 </span></font></div><div><font size="2"><span> 3.224 HA 56.082 CA </span></font></div><div><font size="2"><span> 1.518 HB* 18.860 CB </span></font></div><div><span><font size="2"> </font></span></div><div><font size="2"> 17 D<span> 3 179.378 74 </span></font></div><div><font size="2"><span> 8.451 HN 116.577 N </span></font></div><div><font size="2"><span> 4.370 HA 57.335 CA </span></font></div><div><font size="2"><span> 2.656 HB* 39.698 CB </span></font></div><div><span><font size="2"> </font></span></div><div><font size="2"> 18 V<span> 5 177.276 117 </span></font></div><div><font size="2"><span> 7.579 HN 122.993 N </span></font></div><div><font size="2"><span> 3.720 HA 65.701 CA </span></font></div><div><font size="2"><span> 2.068 HB 31.930 CB </span></font></div><div><font size="2"><span> 1.160 HG1* 22.719 CG1 </span></font></div><div><font size="2"><span> 0.642 HG2* 20.806 CG2 </span></font></div><div><font size="2">..........................<span> </span></font></div><font size="2"></font>
Example2.2. Assigned AA-fragments without user ID specified.
<div><font size="2">.........................</font></div><div><font size="2"> 10 G<span> 2 174.136 </span></font></div><div><font size="2"><span> 8.605 HN 110.399 N </span></font></div><div><font size="2"><span> 3.708 HA* 46.225 CA </span></font></div><div><span><font size="2"> </font></span></div><div><font size="2"> 11 T<span> 4 174.109 </span></font></div><div><font size="2"><span> 8.114 HN 113.206 N </span></font></div><div><font size="2"><span> 4.325 HA 61.900 CA </span></font></div><div><font size="2"><span> 4.283 HB 69.855 CB </span></font></div><div><font size="2"><span> 1.126 HG2* 21.639 CG2 </span></font></div><div><span><font size="2"> </font></span></div><div><font size="2"> 12 N<span> 1 175.100 </span></font></div><div><font size="2"><span> 8.231 HN 122.327 N </span></font></div><div><span><font size="2"> </font></span></div><div><font size="2"> 16 A<span> 2 179.269 </span></font></div><div><font size="2"><span> 3.224 HA 56.082 CA </span></font></div><div><font size="2"><span> 1.518 HB* 18.860 CB </span></font></div><div><span><font size="2"> </font></span></div><div><font size="2"> 17 D<span> 3 179.378 </span></font></div><div><font size="2"><span> 8.451 HN 116.577 N </span></font></div><div><font size="2"><span> 4.370 HA 57.335 CA </span></font></div><div><font size="2"><span> 2.656 HB* 39.698 CB </span></font></div><div><span><font size="2"> </font></span></div><div><font size="2"> 18 V<span> 5 177.276 </span></font></div><div><font size="2"><span> 7.579 HN 122.993 N </span></font></div><div><font size="2"><span> 3.720 HA 65.701 CA </span></font></div><div><font size="2"><span> 2.068 HB 31.930 CB </span></font></div><div><font size="2"><span> 1.160 HG1* 22.719 CG1 </span></font></div><div><font size="2"><span> 0.642 HG2* 20.806 CG2 </span></font></div><div><font size="2">.......................... </font></div><font size="2"></font>
3. CYANA chemical shift file (prot-file)
<div</div>
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
...............................