[chimerax-users] The problem of ligands disappearing when the file is converted

[Elaine Meng]

Hi Kenji,
I don't really know how to use Pymol very well, so I can't help with that program. 

However, my only guess is that in ChimeraX, you did not correctly combine the receptor and ligand models into one model before saving it as a PDB file, or that when you saved you didn't save the combined model but some other model.

I happened to have an extremely old version of Pymol on my old computer (it does not run on my current computer), and when I opened result10.pdb saved from your session with exactly the commands I sent you earlier, I could see that the ligand was displayed, see screenshot:

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The reply I sent before with the exact commands that I used to make the file is here:
<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-December/003032.html>

...and I also attach that file, result10.pdb:  
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I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Dec 19, 2021, at 10:14 PM, Kenji MATSUI via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear  ChimeraX
> 
> Thank you very much for your kind words in the past.?When I opened the PDB file and mol2 file saved by pymol using the method you gave me, the ligands disappeared.
> 
> How can I get pymol to display the ligands as well??
> 
> Here is in detail.
> 
> As you suggested, I created a new model by combining #1 and #10, and saved the newly single model in a PDB file. However, when I displayed this file in pymol, I could not see the ligand as shown in the figure.
> <image.png>
> <image.png>
> So we tried to align the ligand OSW-1 to the protein osh4 in this figure, but it was difficult to analyze because OSW-1 was far away from the distance of the protein osh4 as shown in the figure below.
> 
> <image.png>
> 
> 
> Refernece?Save command:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb>
> 
> Also, I've looked at tutorials and other sites on the Internet to try to figure out what's causing this, but no luck!
> 
> I'm sorry for the many questions.
> ---------------------------------------------------------------------------
> Kenji Matsui
>  Graduate School of Tokyo University of Agriculture and Technology
> 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
>  Mail: s214903z at st.go.tuat.ac.jp