[chimera-dev] python script for ligand preparation

[ngayatri]

Hello Elaine Meng,
I have attached a picture of commands that i have been using for ligand
preparation and also i have attached the output of .mol2 output file for your
reference. Please have a look and let me know about the mistake that i have been
making in the commands that i have been using.

Thank You
Regards
Gayatri Navle

On June 22, 2022 at 9:08 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Dear Gayatri,
> It is not possible to know what happened unless you provide more information.
> Did saving the mol2 file work correctly when you entered the "write" command
> directly into the Command Line (when testing before making the script)? If
> not, then you probably typed the wrong command. Exactly what command did you
> use? Were there any error messages? Was the .mol2 file empty? etc.
>
> You could also attach the script if you don't mind making it public. However,
> I don't know python so somebody else would have to look at it. I can only
> advise on the Chimera commands.
>
> I hope this helps,
> Elaine
>
> > On Jun 22, 2022, at 2:56 AM, ngayatri via Chimera-dev
> > <chimera-dev at cgl.ucsf.edu> wrote:
> >
> > Dear Elaine,
> > I followed the steps to save a ligand in .mol2 file but the mol2 format file
> > after saving is not opening in the chimera even after adding the charges.
> > Please help me with what steps should i follow.
> >
> > Thank You
> > Regards
> > Gayatri
> >
> > On June 21, 2022 at 1:47 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > > Hi Gayatri,
> > > There is a Dock Prep tool that does all this. Menu: Tools... Structure
> > > Editing... Dock Prep
> > > <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html>
> > >
> > > If you mean that you have too many files to do individually with the
> > > graphical interface, however, you may need to figure out how do it with
> > > Chimera commands instead. See commands "open" to open the ligand file,
> > > "addh" to add hydrogens, "addcharge" to assign partial charges (and maybe
> > > other commands depending on what you mean by prepare) and"write" to save
> > > Mol2.
> > > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/open.html>
> > > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html>
> > > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>
> > > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
> > >
> > > You should first try entering those individual commands in the Command
> > > Line one by one to figure out exactly what options you want for each
> > > ligand. After you know what commands and options you want to use for each
> > > ligand, then you can put a python script around it to loop through
> > > multiple files as described here
> > > <https://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 Jun 20, 2022, at 4:37 AM, ngayatri via Chimera-dev
> > > > <chimera-dev at cgl.ucsf.edu> wrote:
> > > >
> > > > Dear Chimera Team,
> > > > I am trying to prepare separate ligand file and saving it in the .mol2
> > > > file. So if you could help with script or the approach would be
> > > > grateful.
> > > > Thank You
> > > > Regards
> > > > Gayatri
>
>
> For assimilation and dissemination of knowledge, visit cakes.cdac.in
>
>
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