To prepare it, use ChimeraX menu: Tools... Structure Editing... Dock Prep.  For how to use that tool, please read the help page:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/dockprep.html>

If you don't want a Mol2 file, then just un-check that option in the Dock Prep tool to turn it off.  However, PDB files will not include the charge information.  So if you need charge information in the output file, you have to save Mol2, not PDB.

To save a PDB file, use ChimeraX menu: File... Save, choose "files of type: PDB"

The above explains how to save files using the ChimeraX graphical interface (GUI).  Another way is to use the "save" command to save PDB or Mol2 format, see the command help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#mol2>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Apr 7, 2024, at 10:44 AM, Mokshith Dg via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
>
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