Dhiraj,
Download the command line version of foxs from
https://modbase.compbio.ucsf.edu/foxs/.
You can integrate foxs into linux scripts:
[tannerjj@dizzy ambiguity]$ cat FoXS.sh
#!/bin/bash
date
while read pdb
do
echo "processing " $pdb
/titan/tanner/SAXS/FoXS/foxs --max_q=0.32 $pdb $dat
done < filelist
date
You can also use wildcards: foxs *.pdb *.dat
Type foxs without arguments to get help:
[tannerjj@dizzy ~]$ foxs
/titan/tanner/SAXS/FoXS/foxs
Usage: <pdb_file1> <pdb_file2> ... <profile_file1> <profile_file2> ... :
Options:
--help Any number of input PDBs and profiles is
supported. Each PDB will be fitted against
each profile.
--version FoXS (IMP applications)
Copyright 2007-2016 IMP Inventors.
All rights reserved.
License: GNU LGPL version 2.1 or later
<http://gnu.org/licenses/lgpl.html>.
Written by Dina Schneidman.
-s [ --profile_size ] arg (=500) number of points in the profile
-q [ --max_q ] arg (=0.50) max q value
--min_c1 arg (=0.99) min c1 value
--max_c1 arg (=1.05) max c1 value
--min_c2 arg (=-2.00) min c2 value
--max_c2 arg (=4.00) max c2 value
-h [ --hydrogens ] explicitly consider hydrogens in PDB files
(default = false)
-r [ --residues ] fast coarse grained calculation using CA
atoms only (default = false)
-b [ --background_q ] arg (=0) background adjustment, not used by default.
if enabled, recommended q value is 0.2
-o [ --offset ] use offset in fitting (default = false)
-p [ --write-partial-profile ] write partial profile file (default = false
)
-m [ --multi-model-pdb ] arg (=1) 1 - read the first MODEL only (default), 2
- read each MODEL into a separate structure
, 3 - read all models into a single structu
re
-v [ --volatility_ratio ] calculate volatility ratio score (default =
false)
-l [ --score_log ] use log(intensity) in fitting and scoring
(default = false)
-g [ --gnuplot_script ] print gnuplot script for gnuplot viewing
(default = false)
On Jun 6, 2018, at 1:25 AM, Srivastava, Dhiraj
<[email protected]<mailto:[email protected]>> wrote:
Hi All
sorry for asking non-crystallography related question. Is it possible
to integrate crysol or FoxS in python and pymol? I have generated thousands of
models of my protein that I want to test against SAXS and other biochemical
data. The ability to integrate the comparison of experimental and calculated
X-ray scattering profile into python and pymol will be really helpful as I can
easily calculate other parameter of my protein in pymol and compare it to other
biochemical data. There is a pymol plugin available for SAXS but its not
helpful for me as its not practical to use plugins for so many different
models. I am looking for script that can automate the calculation.
if anyone has script that can do this and is willing to share with
me, that will be really helpful.
thank you
Dhiraj
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John J. Tanner, PhD
Professor of Biochemistry and Chemistry
Interim Chair, Department of Biochemistry
University of Missouri-Columbia
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Email: [email protected]<mailto:[email protected]>
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