[Chimera-users] PyChimera addCharge

[Matas Tiskus]

Thank you!
I made it work.

Matas

2020-10-15, kt, 19:13 Elaine Meng <meng at cgl.ucsf.edu> rašė:

> In case you didn't already know, PyChimera has its own User Guide here:
>
> <https://pychimera.readthedocs.io/en/latest/>
>
> PyChimera is developed by our friends in Barcelona (Maréchal group).
>
> For examples, Joe Healey has some PyChimera scripts on github, but they
> may not be similar to what you want to do:
>
> <https://github.com/jrjhealey/chimera>
>
> Elaine
>
> > On Oct 15, 2020, at 8:52 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > Hi Matas,
> > I don't know if you need pychimera to do it.  Seems like you could just
> do it with Chimera commands "addcharge" (with "addh" first if the
> structures didn't have hydrogens) and "write" with the "format mol2" option.
> >
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
> >
> > Figure out which commands and their options work the way you want, and
> then see here for how to use python to loop through input files and apply
> Chimera commands to each:
> > <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html
> >
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >> On Oct 15, 2020, at 3:39 AM, Matas Tiskus <tiskusm at gmail.com> wrote:
> >>
> >> Hello,
> >> I was looking for ways to add charges to protein structures in a python
> script and write a .mol2 file. I believe it is possible to do with
> importing pychimera into the script, but i can't seem to make it work. How
> would the code for this purpose look like?
> >> Matas
> >
> >
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>
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