[Dock-fans] Is there a way to separate the mol2 files in poses.mol2

lingling Jiang jianglilian68 at gmail.com
Thu Jul 14 08:13:04 PDT 2016

Hi Jonathan,

Although the different poses are saved together in one multi-mol2
file, the format of the file is rather simple. If you open it in vim,
you should find that different poses are written in separate sections,
each includes header and footer. It should be very straightforward to
write a script to split the multi-mol2 file into separate mol2 files
by simply searching for keywords in the header/footer.

Also, you can try open and manipulate the multi-mol2 file using
molecular modeling softwares such as VMD or Chimera. You might want to
check their tutorials for further instructions.

Hope this helps,

On Thu, Jul 14, 2016 at 10:47 AM, Jonathan Gough
<jonathan.d.gough at gmail.com> wrote:
> Hi,
> After having done a docking expt and enrichment expt using the
> combineScoresandPoses.py script you get a very large mol2 file that
> wonderfully has all the poses together. I was wondering, Is there a way
> within the other wonderful scripts you have put together to extract each of
> the mol2 poses from the combined poses.mol2 file? Or can someone point me in
> the right direction towards some code in the scripts to look at in terms of
> trying to figure out how to write something like that for myself?
> thanks,
> Jonathan
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Lingling Jiang
Postdoctoral Research Scientist, Tavazoie Lab
Dept. of Systems Biology, Columbia University

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