Re: [PyMOL] How to draw clashes in pymol

Hi Bondurant,

I really like the merging of the graphic beauty of pymol with the detailed
depictions of reduce and probe.  I have a method that is a bit clunky for
doing what you ask, but I don't know if it ever made it to the mainstream
in MolProbity.  The caveat of wanting to work with a ligand makes it a bit
harder to explain so my apologies in advance if things aren't 100% clear
but here goes....

1. Make sure you have a reduce definition file for your ligand.  If the
ligand had been deposited in the PDB before ~2012 then the
reduce_wwPDB_het_dict file found (
http://kinemage.biochem.duke.edu/software/reduce.php)  should have it,
otherwise here's an example:

RESIDUE   ACP      11
CONECT      P      4 O1   O2   O3   O4
CONECT      O1     1 P
CONECT      O2     1 P
CONECT      O3     1 P
CONECT      O4     2 P    C1
CONECT      C1     3 O4   O5   C2
CONECT      O5     1 C1
CONECT      C2     4 C1  HC1  HC2  HC3
CONECT     HCH1    1 C2
CONECT     HCH2    1 C2
CONECT     HCH3    1 C2
END
HET    ACP              8
HETNAM     ACP ACETYL PHOSPHATE
FORMUL      ACP    C2 H3 O5 P1 2-

2. download the reduce and probe executables also from
http://kinemage.biochem.duke.edu/

3.  run reduce make sure to use the -DB flag to input your ligand dictionary

4. run probe with a command something like:
probe -both "chaina 88 (ATOM_OG1 | ATOM_HG1)" "chainx 1" CheY_A88T_AcP_H.pdb
Where chain A in this case is the protein and the hydroxyl of Thr 88 is the
only relevant interacting group with chain X the ligand.

5. convert the probe output to a python script to render the cgo objects in
pymol using the attached perl script.  ./probe_to_cgo [input probe dots]
[output pymol cgo]

6. use the run command in pymol to execute the python script and draw the
cgo output.

If this all works the first go then amazing!  If not I can try to help get
things working, but it's been a few years since I last used these tools.

Best of Luck!
-bob



On Fri, Aug 29, 2014 at 10:30 AM, Bondurant <bon...@gm...> wrote:

> Hello community,
> I would like to draw a figure similar to this one
> http://www.cell.com/cms/attachment/615980/4968633/gr1.jpg
> showing the clashes between a potential ligand and the protein. The only
> way i know how to do this in pymol is using the show_bumps plugin, but i
> don't really like the "red disks" format.
> Could anyone tell me how i could easily draw something similar to those
> red spikes from the example to represent the clashes in pymol or any other
> program? I'm able to do it using molprobity and kinemage, but there's no
> much possibilities for editing and to get it in printing quality.
> Thanks
>
>
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