IMP
2.2.0
The Integrative Modeling Platform
|
The integrative docking protocol includes a number of tools:
<pdb1> - The first molecule that was given to docking program and was kept in place during docking <pdb2> - The second molecule that was given to docking program and was transformed <trans_file> - Docking output file with transformations that bring the transformed molecule to the static molecule. The format is as follows:
1 -0.75020 0.67870 0.34160 82.62000 59.28000 -1.01100 2 -0.42560 0.55540 0.33110 75.69000 67.15000 -0.30480 3 -0.48910 0.66950 0.11820 84.94000 58.97000 3.34300
The first number is the transformation number followed by three rotational and three translational parameters.
<exp_profile_file> - The SAXS profile of the complex. see http://modbase.compbio.ucsf.edu/foxs/help.html for format details.
<pdb1> <pdb2> <trans_file> as above <image1> <image2>... - complex 2D class averages in PGM format (P2)
<pdb1> <pdb2> <trans_file> as above <em_map> - density map of the complex in mrc format
<pdb1> <pdb2> <trans_file> as above <residue_content_file1> - residue content file for pdb1 or '-' if none <residue_content_file2> - residue content file for pdb2 or '-' if none The format of the file is as follows:
MET 0 ARG 0 HIS 2
This would correspond to having 0 methionine, 0 arginine and two histidine residues in the interface.
<pdb1> <pdb2> <trans_file> as above <cross_links_file> - file with detected cross links
The format of the file is as follows: 145 - 1 A 3 27 224 - 1 A 3 27 169 - 1 A 3 27 222 - 1 A 3 27
Each line corresponds to one cross link. Each cross link is defined by residue numbers and chain ids of the cross linked residues, followed by limits on the distance between CA atoms.
'145 - 1 A 3 27' corresponds to a cross link between residue 145 in a chain with blank chain id and residue 1 in chain A. The minimal distance is 3A and the maximal is 27A.
# | score | filtered (+/-) | z-score | ... | Transformation
The programs for scoring of docking transformations (saxs_score, em2d_score, em3d_score, nmr_rtc_score) output results in this format.
Only filtered values of + are combined. The output score is the weighted sum of Z-Scores.