[Chimera-users] Splitting the ligand cluster file

[Elaine Meng]

Hello Saptarshi!
If you could already see the ligands one by one with ViewDock, they are already separate models (something like #0.1, 0.2, … 0.N) and there is no need to split.  Just use menu: File… Save PDB and in the “Save models” list, choose the model number (e.g. #0.25) of the binding mode you want to save.  Save PDB dialog: 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>

The specific model number is shown in the ViewDock dialog when you are viewing binding modes one by one; for example, in this image it is #2.1.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/viewdock.html#listbox>

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

> On Apr 11, 2018, at 12:11 AM, SAPTARSHI MUKHOPADHYAY 14BBT0011 <saptarshi.mukhopadhyay2014 at vit.ac.in> wrote:
> 
> Hello! 
>             I recently performed a ligand-protein docking job in SwissDock and downloaded the output file which contained the "clusters.dock4.pdb" file. I performed the ViewDock analysis on Chimera and now want to save a specific binding mode of a ligand  from the cluster. I understand that the "Split" function is to be used in this regard, but I am not sure on how to implement this because of my limited experience with Chimera. Can I be provided with the exact steps for using this function?
> 
> Thanks,
> 
> Regards,
> Saptarshi