[Dock-fans] Refining Dock output

John J. Irwin jji at cgl.ucsf.edu
Tue Jul 15 15:28:37 PDT 2008


Hi Diwan

You can also do it without Pipeline Pilot in plain old linux:

grep -n '@<TRIPOS>MOL' output.mol2|tail -n +3001|head -1| sed 's/:.*$//' >! cut
@ CUT = `cat cut` - 1
head -$CUT output.mol2 >! new.mol2

Happy docking.

John
UCSF DOCK Team

Todd Wipke wrote:
> Sure, convert to SDF file, use Pipeline Pilot and put 3000
> in the "Maximum" parameter, then do whatever you want with
> them, e.g., write to an SDF file.  You can also use the
> Student Edition of Pipeline Pilot which is free to
> academics.
> -Todd
>
> On Tue, 15 Jul 2008, Abdul Hameed, MohamedDiwanMo wrote:
>
>   
>> Hello everyone,
>>
>> I did a docking study and have some 8000 docked/ranked molecules as output.
>> I would like to retain only the first 3000 molecules from these ranked ligands. Can anyone tell me how I can do it?
>> Is it possible to take only the top 3000 molecules from this output set?
>> Any suggestions will be helpful.
>>
>> Thank you,
>> Diwan
>>
>>     
>
> W. Todd Wipke, Ph.D.
> Professor of Chemistry and Biochemistry
> Molecular Engineering Laboratory
> University of California                 voice 831-459-2397
> Santa Cruz, CA  95064                    fax   831-459-2395
> http://chemistry.ucsc.edu/wipke_w.html
>
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>   


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