[Chimera-users] Multiple Docking Using Chimera

Elaine Meng meng at cgl.ucsf.edu
Mon May 2 16:44:21 PDT 2016


Hi Turki Sobahy,
Chimera only knows how to read the various pieces of information if you are using one of docking output formats it understands.  These formats are listed in the ViewDock manual page:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html>

I don’t know what docking program you are using or what format of output you are reading into Chimera, so I can’t really say anything other than it should be in one of those formats. It seems like it must be in one of those formats if you are getting a ViewDock table. It might be that the names are read but not initially shown in the table.  In that case you might be able to show them by just choosing some option from that dialog’s “Column” menu.  If not, we would need an example file including a few ligands to be able say anything else.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco



> On May 2, 2016, at 12:11 AM, SOBAHY, TURKI MOHAMMED <tsobahy at kfshrc.edu.sa> wrote:
> 
> Hello,
> 
> I have a protein of interest that I need to perform molecular docking on by multiple ligands (~1000,000).
> 
> The protein is in PDB file format, while ligands are in a SDF file format.
> 
> Initially, the ligands were divided into multiple SDF files (mini) for hardware sake. 
> Then, a python script was developed to handle the docking of each mini SDF file against the protein of interest.
> 
> This works nicely, however docking scores (tables) have no ligands IDs associated to distinguish each score.
> 
> So, basically I have scoring tables without any key IDs!!
> 
> Kindly, I want to know if you have encountered the same problem and what approach you took to solve this.
> 
> Thanks,​
> ______________________________
> Turki Sobahy
> Research Associate
> Research Center (J-04)
> King Faisal Specialist Hospital
> & Research Center (Gen.Org.)-Jeddah Branch 
> PO Box 40047, Jeddah 21499, Saudi Arabia
> Tel# +966 667 7777 ext. 66736| MCD# 40716
> Mobile# +966 505837027
> email tsobahy at kfshrc.edu.sa
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