HI Thomas,
I have a protein with two chain A and B. both have only one ligand in them.
As I explained before, I want to identify the size of the pocket , and also
I replace the ligand with another ligand that I have ,
do you know how I do it?
Many thanks
Mohammad
On Sun, Jul 16, 2017 at 3:58 PM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:
> Hi Mohammad,
>
> If there is already a ligand in the pocket and you just want to know its
> center x,y,z, you can simply type:
>
> centerofmass organic
>
> Or if there are multiple organic molecules and you are interested in one
> with the unique residue name "LIG":
>
> centerofmass resn LIG
>
> I wound't call that "finding" a pocket though.
>
> Cheers,
> Thomas
>
> > On Jul 11, 2017, at 7:42 PM, Mohammad Goodarzi <
> mohammad.goda...@gmail.com> wrote:
> >
> > Hello,
> >
> > I am wondering whether it is possible to find the pocket of a protein in
> Pymol?
> > lets say I have a protein and a ligand inside the pocket. I want to
> estimate the x, y and z
> >
> > Best Regards,
> > Mohammad
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
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