Hello Joern, As far as I can recall, Autodock Vina will (or at least has a choice to) put all the ligand docking results, i.e. multiple poses and/or compounds, in a single pdbqt file. I don't have the program currently, so I can't say anything specifically about how to control it.

If all you have now is a lot of separate models, you could try opening them all, and then saving them to a single multi-model PDB file and reopening that single PDB file with ViewDock. However, that would lose all of the extra information in the pdbqt file, certainly the charge/radius columns, and also perhaps all of the scores and other other descriptors output by docking. Thus it would be better if you could get the single-file output directly from the docking program.

saving PDB files from Chimera https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb

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

On Mar 19, 2022, at 5:05 AM, Joern Werner via Chimera-users chimera-users@cgl.ucsf.edu wrote:

Hello

is there a way of reading a series of pdbqt files of docked ligands using vina dock externally back into chimera for inspection and analysis? It looks like Viewdock, should do this but I have a directory full of individual ligand files and I don't know how to prepare them so that Listview reads them into an ordered set i.e. ligand1 ligand2 etc. I can read individual ligands fine.

Many thanks Joern _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users