The input data for LGA processing is composed from
two sets of 3D structures (atom coordinates for molecule1 and molecule2).
As the result of LGA calculations the coordinates of the molecule1 will
be rotated.
By default the calculations are performed on CA atoms. However, user can
select other than CA atoms or define position within residues on which the
superposition will be calculated (see example2, example4 below, and LGA parameters: "-atom","-bmo", and "-cb").
The list of molecules has to be prepared in the following format:
PDB_entry [Name [Class [Parameters]]]
where: PDB_entry - PDB code (entry) of the chain from PDB, or local structure
Name - name you would like to use on the plot (optional)
Class - additional comment (e.g. class from SCOP) (optional)
Parameters - LGA parameters for particular molecule (e.g. selected range
or chain) (optional)
For information about "Parameters" please check LGA parameters.
In your list you can combine the following formats:
PDB_entry
or
PDB_entry Name
or
PDB_entry Name Class
or
PDB_entry Name Class Parameters
Please make sure that you select PDB entry (chains, domains) correctly.
Otherwise NO RESULTS will be calculated.
PDB_entry has to be in the following format:
1cpi_A for PDB entry: 1cpi, chain: 'A'
1akf for PDB entry: 1akf, chain: ' '
1ggg* for PDB entry: 1ggg, all existing chains are selected (chain 'A' and 'B')
or specifying NMR MODEL:
1bve_B_5 for PDB entry: 1bve, chain: 'B', model: 5
1rel___4 for PDB entry: 1rel, chain: ' ', model: 4
There are several ways how to select from given structures the set
of residues for calculations.
Here are some examples:
-ch1:B - chain B from molecule1 is selected
-er1:B:B - chain B from molecule1 is selected
-aa1:1:317 - residues 1 till 317 from molecule1
-gap1:152:156 - remove residues 152 - 156 from molecule1
-aa1:45:361 - residues 45 till 361 from molecule1
-er1:45_B:50_B - residues 45 till 50 from molecule1 chain B
-er1:7S_B:7_C,12_C:49_C - selects two ranges in molecule1: the residues 7S_B (residue 7
insertion S from chain B) up to 7_C (residue 7 from chain C)
and residues 12 till 49 from chain C
Parameters for LGA calculations for comparison of CA or CB positions in identical residues (column: GDC_at):
-gdc_at:V.CA,L.CA,I.CA,P.CA,M.CA,F.CA,W.CA,S.CA,T.CA,C.CA,Y.CA,N.CA,Q.CA,D.CA,E.CA,K.CA,R.CA,H.CA,G.CA,A.CA
or
-gdc_at:V.CB,L.CB,I.CB,P.CB,M.CB,F.CB,W.CB,S.CB,T.CB,C.CB,Y.CB,N.CB,Q.CB,D.CB,E.CB,K.CB,R.CB,H.CB,G.CB,A.CB
Example1 of the PDB list (simple; selected chains):
Copy and paste the PDB list:
1br6_A
1abr_A
1j1m_A
1m2t_A
1pum_A
1onk_A
1hwn_A
2q3n_A
1gis_A
1ahc_A
1nli_A
1cf5_A
1nio_A
2oqa_A
1bry_Y
Name of the PDB chain (reference structure):
1br6_A
Example2 of the PDB list (simple; selected chains, calculations using CB positions):
Parameters for LGA calculations:
-4 -d:4.0 -cb:1.0 -atom:CB -swap
Copy and paste the PDB list:
1br6_A
1abr_A
1j1m_A
1m2t_A
1pum_A
1onk_A
1hwn_A
2q3n_A
1gis_A
1ahc_A
1nli_A
1cf5_A
1nio_A
2oqa_A
1bry_Y
Name of the PDB chain (reference structure):
1br6_A
Example3 of the PDB list (advanced; selected chains and ranges):
Copy and paste the PDB list:
5p21_A unique_name
1ii5_A 1ii5_chain_A class
1gnp_A 1gnp_gaps c.37.1.8 -er1:10_A:30_A,60_A:70_A,90_A:100_A
1wdn_A 1wdn_A_12_60 c.94.1.1 -er1:12_A:60_A
1qd6* d1qd6_1 f.4.2.1 -er1:A:A -er1:C:C
1o7d* d1o7d_1 a.8.3.1 -er1:385_B:421_B -er1:431_C:487_C
Name of the PDB chain (reference structure):
1hiv_A
Example4 (advanced; two proteins (1abr_A and 1br6_A) are compared in the selected region
using different point representation of amino-acids (points from the vector Ca-Cb)).
Parameters for LGA calculations:
-3 -d:2.0 -atom:CB -er1:85_A:106_A -er2:91_A:94_A,96_A:97_A,100_A:111_A,113_A:116_A
Sorting parameter:
Name
Copy and paste the PDB list:
1abr_A 01_1abr__10 abrin -cb:-1.0
1abr_A 02_1abr__08 abrin -cb:-0.8
1abr_A 03_1abr__06 abrin -cb:-0.6
1abr_A 04_1abr__04 abrin -cb:-0.4
1abr_A 05_1abr__02 abrin -cb:-0.2
1abr_A 06_1abr_00 abrin -cb:0.0
1abr_A 07_1abr_02 abrin -cb:0.2
1abr_A 08_1abr_04 abrin -cb:0.4
1abr_A 09_1abr_06 abrin -cb:0.6
1abr_A 10_1abr_08 abrin -cb:0.8
1abr_A 11_1abr_10 abrin -cb:1.0
1abr_A 12_1abr_12 abrin -cb:1.2
1abr_A 13_1abr_14 abrin -cb:1.4
1abr_A 14_1abr_16 abrin -cb:1.6
1abr_A 15_1abr_18 abrin -cb:1.8
1abr_A 16_1abr_20 abrin -cb:2.0
1abr_A 17_1abr_22 abrin -cb:2.2
1abr_A 18_1abr_24 abrin -cb:2.4
1abr_A 19_1abr_26 abrin -cb:2.6
1abr_A 20_1abr_28 abrin -cb:2.8
1abr_A 21_1abr_30 abrin -cb:3.0
Name of the PDB chain (reference structure):
1br6_A