[Dock-fans] Re: Dock-fans Digest, Vol 14, Issue 15

Jose A zyclopia at gmail.com
Fri Aug 26 08:50:22 PDT 2005

you sound like you have more than one molecule in your out_scored.mol2
file. some programs like chimera allow you to see all compounds at the
same time or toggle through them when they are read in a single file
(as in out_scored.mol2), but some programs can't do this (pymol?. i
know setor can't) and so you have to write a separate file for each
molecule you want to visualize.

of course if you have hundreds of molecules it won't be a lot of fun
to create separate files for each. is there software that can do this?
split a many molecule file into single ones? (I can't quite recall but
i feel I have read about this)

the other side of this is that you want to rank the molecules first
(with chimera for example), so you can look through the top scoring
compounds and not thousands or more.  the rank keyword in DOCK... It
hans't worked for me yet. I thought it was fixed for v5.2...was it?
isn't it supposed to tell DOCK to do this for us?

on a final note, if you are trying to DOCK a single molecule or just a
few, you can play with the write_orientations/write_conformations
command. if you turn these on (set to yes) you will write all the
orientations and conformations FOR EACH MOLECULE docked. of course,
this can lead to huge files fairly quickly...

> Hello dock-fans!
> I am getting as out_scored.mol2 file a file with some molecules and when I open it with pymol (for example) I can see one molecule. Is this the molecule with the hightest score ? how can I see the other?
> Best Regardes
> Oshik Segev

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