[Dock-fans] out_scored.mol2 file

Philip Crawford p.crawford at unsw.edu.au
Wed Aug 31 16:41:38 PDT 2005

Hi. I've been using the ZINC database with Dock 5.2, cutting into small
chunks for processing. 
I just found Chimera (also from UCSF), which can read in your
out_scored.mol2 file and sort (in my case by Energy, vdw, es, or name). It
can then save the sorted file. In Chimera, you need to open your
macromolecule, then go to Tools | Docking | ViewDock and open your scored
output file. Here, you can step through the
For ranked output, you need to give a number of molecules to rank in your
input file. I haven't been using RMSD, so ranking has been done by Energy.
I've been asking for 10% in ranked_output.mol2 file as in:
max_ligands                                                  500
rank_ligands                                                 yes
max_ranked_ligands                                           500

Hope this helps.
Chimera is written in Python and  installs its own copy of Python, which
seems to be 2.3.
Philip Crawford, B. Comp. Sc., MIEEE
Structural BioInformatics and Drug Design Group
School of Medical Sciences
The University of NSW
Phone: +61-2-9385 2564
Mobile: +61-419-294 698
Fax: +61-2-9385 1059
Email: p.crawford at unsw.edu.au


From: dock-fans-bounces at docking.org [mailto:dock-fans-bounces at docking.org]
On Behalf Of oshik segev
Sent: Wednesday, 31 August 2005 4:48 PM
To: Dock-fans at docking.org
Subject: [Dock-fans] out_scored.mol2 file

Hello dock-fans!
I'm having problems with the output files I am getting. I'm running DOCK5 on
a subset from ZINC database and I allways get an output file with many
molecules in the out_scored file. Are the molecules in this file ranked? How
can I rank them, by the energy score or by the RMSD? (In my input file the
parameter out_ranked is YES and I get an empty file). 
Thank you
Oshik Segev
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