[chimerax-users] Question: PDB file creation

[Kenji MATSUI]

Dear Elaine C. Meng and   ChimeraX

I apologize for the mistake in sending the email to the wrong address.
Thank you for your quick response and polite reply. I will try it as soon
as possible. I look forward to working with you again in the future.

---------------------------------------------------------------------------
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


2021年12月18日(土) 4:20 Elaine Meng <meng at cgl.ucsf.edu>:

>
> Begin forwarded message:
>
> *From: *Kenji MATSUI <s214903z at st.go.tuat.ac.jp>
> *Subject: **Question: PDB file creation*
> *Date: *December 16, 2021 at 7:20:41 PM PST
> *Cc: *Kaori Sakurai <sakuraik at cc.tuat.ac.jp>
>
> Dear UCSF ChimeraX
>
> Thank you for allowing me to use your software. I am Japanese, so I hope
> you will understand that there are some inappropriate expressions. I would
> like to ask you two questions.
>
> First, I would like to know how to convert a cxs file saved in Chimera X
> to a PDB file.
>
> Aim
> To display the interaction between a protein (osh4) and a ligand (OSW-1)
> in pymol
>
> Methods I have tried
> I found a way to convert mmCIF to PDB file, but I could not find a site
> to convert cxs file to PDB file.
>
> Second, How to deal with the following error that appears when the
> structure of the osh4-OSW-1 complex is shown.
>
> APBS electron
> Error: The following residues are missing heavy (non-hydrogen) atoms,
> which may result in inaccurate electron density.
> Thank you for your cooperation.
>
> ------------------------------------------------------------
> ---------------
> 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
>
>
> Hi Kenji,
> I omitted your cxs file from this message since I thought maybe you wanted
> to keep it private (messages on this chimerax-users at cgl.ucsf.edu mailing
> list can be seen by the public).
>
> I didn't see that APBS error when I opened the cxs file in ChimeraX.  It
> appears to be a message from another program (not ChimeraX): the APBS
> program, which calculates electrostatic potential.  The error is exactly
> what it says: some residues in the structure are missing some atoms, which
> would affect the calculation of electrostatic potential values.
>
> Short answer #1 is why not look at the interactions in ChimeraX instead of
> Pymol?  You can calculate H-bonds, find contacts, etc.  See this tutorial,
> for example
> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html
> >
>
> Short answer #2 is that you can open the session (cxs) file in ChimeraX
> and then save a PDB file with the "save" command or the menu: File...
> Save... (choose Files of type: PDB).
>
> HOWEVER, a longer answer may be required here because I can see from
> opening your cxs file that it contains many models, I guess a receptor
> (model #1) and ligands from docking (models #2-258) with only some ligands
> displayed (models #10-17).
>
> I'm guessing you want to save only the ones that are displayed.  You could
> save models #1,10-17 into one multi-model PDB, file but probably for
> analysis in Pymol or other programs, you would instead need to  combine
> each ligand with receptor and save it separately.  In other words, you may
> need to make a new model by combining #1 with #10, and then save the new
> single model to a PDB file.  For example:
>
> combine #1,10 modelId #300
> save /Users/meng/Desktop/result10.pdb models #300 relModel #1
>
> Then repeat for other ligands, combining #1 with #11 to make a new model
> and saving that new model, combining #1 with #12, etc.  See the help links
> below for the options of each command.
>
> Save command:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb>
> Combine command:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
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