[Chimera-users] problem with pdb file saved from chimera-autodock vina analysis

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 3 08:40:29 PST 2021

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:

I hope this helps,
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 at 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
> 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 at uq.edu.au
> <Brevi_Cry_3_CGTi.pdb><BREVI_CRY_3_CGTI_DISCOVERY_PROTEIN_CGT_A_463.pse>_______________________________________________
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