Hi Elaine thank you for your kind update:).

Does Chimera have a simple webpage where you can just click in the pdb and click the output for the Mol2 file
or must there be a download for this?  I could not find the former.

Thanks if you know:),
Joel 🚀

On Thu, Dec 28, 2023 at 8:52 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Joel,
Firstly, UCSF Chimera and UCSF ChimeraX are two different programs.  You sent this question to the ChimeraX questions address.  If you want to ask Chimera questions, please use chimera-users@cgl.ucsf.edu

However, both programs can read PDB and save Mol2.  They can also add hydrogens and assign atomic partial charges which would be included in the Mol2 that you subsequently save, but I don't know if you needed/wanted to do that. If not, just open the PDB file and then save the atomic structure to a Mol2 file.

Since you asked on the ChimeraX list, I'll answer for ChimeraX.

First you open the PDB file with the "open" command (or menu: File... Open if local file, or File... Fetch by ID if it's an entry in the Protein Data Bank).  See help for details:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html>

Then you can save a Mol2 file with the "save" command or menu File... Save, choosing "Files of type: Mol2".  See help for details: 
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#mol2>

If you wanted to add hydrogens and charges before saving, see the Dock Prep tool:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/dockprep.html>

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 Dec 28, 2023, at 11:30 AM, Joel Subach via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> *pdb
>
> On Thu, Dec 28, 2023 at 8:30 PM Joel Subach <mjsubach@alumni.ncsu.edu> wrote:
> ...meaning do you have an easy access method towards the above message as Open Babel does
> i.e. not having to download anything to convert the pdf to a mol2?  Thanks:)
>
> On Thu, Dec 28, 2023 at 8:19 PM Joel Subach <mjsubach@alumni.ncsu.edu> wrote:
> Hello Chimerax, I hope you're well:).
>
> Towards the above subject, SwissParam has recommended UCSF Chimera
> to convert my pdb to a Mol2 File for SwissParam subsequent parameterization,
> however, I could not discover this webpage within your UCSF Chimerax Website?
> Thanks if you can clarify how I may generate this Mol2 via yout Chimera if able.
>
> Best,
> Joel 🚀