Hi Joel,
Both Chimera and ChimeraX are programs you would need to download.  They are not web servers.
Best,
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 12:01 PM, Joel Subach via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> 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 🚀
>
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