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....> 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@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