Re: [ccp4bb] crysol or FoxS integration into python and pymol

[Tanner, John J.]

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:   ...   ... :

Options:
  --helpAny 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
.
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 
mailto:dhiraj-srivast...@uiowa.edu>> 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
117 Schweitzer Hall
503 S. College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-2754
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html







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Re: [ccp4bb] crysol or FoxS integration into python and pymol

[amin sagar]

Hi. If you really want to use a python based script, then you can probably
look at IMP (https://integrativemodeling.org/). However, would it not work
if you download FOXS and run it on thousands of models automatically.
Regards,
Amin.


On Wed, Jun 6, 2018 at 8:25 AM, Srivastava, Dhiraj <
dhiraj-srivast...@uiowa.edu> 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
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] crysol or FoxS integration into python and pymol

[Srivastava, Dhiraj]

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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