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

lingling Jiang jianglilian68 at gmail.com
Thu Jul 14 08:24:01 PDT 2016


Try Chimera ViewDock.

On Thu, Jul 14, 2016 at 11:18 AM, Jonathan Gough
<jonathan.d.gough at gmail.com> wrote:
> Thanks,
> Yes, I have looked at the file and am familiar with it's format. that being
> said I wanted to check and see if something already existed before I went
> ahead and re-invented the wheel. FWIW, vmd will only open a single pose.
>
> Jonathan
>
>
> On Thu, Jul 14, 2016 at 11:13 AM, lingling Jiang <jianglilian68 at gmail.com>
> wrote:
>>
>> 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,
>> Lingling
>>
>> 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
>> >
>> > _______________________________________________
>> > Dock-fans mailing list
>> > Dock-fans at docking.org
>> > http://mailman.docking.org/mailman/listinfo/dock-fans
>> >
>>
>>
>>
>> --
>> Best,
>> Lingling Jiang
>> Postdoctoral Research Scientist, Tavazoie Lab
>> Dept. of Systems Biology, Columbia University
>
>



-- 
Best,
Lingling Jiang
Postdoctoral Research Scientist, Tavazoie Lab
Dept. of Systems Biology, Columbia University


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