Hi Amol, I don't use these other programs (PLIP and Pymol), so I can only guess and try to make suggestions about the Chimera part. Probably you should combine the ligand model and the receptor model into one model before saving a PDB from Chimera. For example, if your receptor model is #0 and the ligand pose that you want is model #1.8: (1) show the Model Panel (menu: Favorites... Model Panel) (2) in the right side of the Model Panel, click on function "copy/combine" (3) in the copy/combine dialog "Molecules to combine/copy", choose only the two models to combine: click #0 to choose receptor, Ctrl-click #1.8 to also choose the ligand pose without unchoosing receptor. Then use this dialog to create new model #2. (4) save your new model #2 as PDB from Chimera and use it for analysis in these other programs Model Panel and its functions: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> 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 2, 2021, at 9:04 PM, Amol Ghodke <a.ghodke@uq.edu.au> wrote:

Hi, First of all thank you so much for making such a wonderful tool and sharing it freely with scientific community. I have been using chimera for sometime now and performed docking analysis using autodock vina. I recently come across a problem. After exporting pdb file with desired docking pose, I tried to run protein ligand interaction analysis on PLIP server. But ligand in my file does not get recognised for analysis.

I opened pdb file in a text editor and upon looking care fully I see chimera saves receptor and ligand as separate model like this ATOM 7453 HD2 PRO A 462 15.986 11.983 20.450 1.00 0.00 H ATOM 7454 HD3 PRO A 462 16.532 10.334 20.885 1.00 0.00 H ENDMDL MODEL 2 HETATM 1 S1 CGT A 1 9.051 5.106 43.099 1.00 0.00 S HETATM 2 C6 CGT A 1 8.150 3.680 42.370 1.00 0.00 C

After comparing it with the pdb file from pbd database I removed “ENDMDL” and “MODEL 2” and re-ran the PLIP analysis. This time it works but PLIP also mentions that – <DB3849EB1C2F41DD9D612071160965BD.png> Analysis went well but the .pse file that I get from PLIP server does not allow me to show ligand in stick format in Pymol software. I suspect this is due to the original pdb file format. I also noticed that pdb file when opened in pymol shows ligand and receptor as different states which is not correct (if I am right). I have attached both original pdb file that I saved from Chimera-autodock vina and pse file from PLIP analysis. May I request to help me resolve this issue? Please let me know if you need any further information or clarification.

Thanks for your time and support Amol

--------------------------------------------------------------------------------------------------------------------------------------------------------- Dr Amol Bharat Ghodke | Post-Doctoral Research Fellow

Queensland Alliance for Agriculture and Food Innovation Level 3, Queensland Bioscience Precinct [#80] Room 3.318, 306 Carmody Rd, St Lucia The University of Queensland St Lucia, Brisbane Qld 4072, AU E. a.ghodke@uq.edu.au

<Brevi_Cry_3_CGTi.pdb><BREVI_CRY_3_CGTI_DISCOVERY_PROTEIN_CGT_A_463.pse>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users