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

[Elaine Meng]

In ChimeraX you have to use the "combine" command to make a new model, and then save the new model.  There is no GUI for combining yet.  After combining, then you can use either the "save" command or menu: File... Save to save the new model.

My example used commands for both steps:
<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-December/003032.html>

Elaine


> On Dec 20, 2021, at 9:46 AM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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:
> 
> <Screen Shot 2021-12-20 at 9.32.17 AM.png>
> 
> 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:  <result10.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 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
> 
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