Hi Rams,
You could consider using LigPlot+, generate LigPlots for all 'n' PDB files,
and then also superimpose all the plots to see the variations in the
protein-ligand interactions of the same ligand bound to different proteins.
Alternatively, you could try to write a program using Coot's lsq li
Hi Rams,
It's also worth looking into the Cambridge CSD suit. I'm pretty sure that there
is a routine there for superimposing small molecules, i.e. ligands which will
produce the matrices you need. How to put it on a script is another question.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Scie
Behalf Of Subramanian,
Ramaswamy
Sent: Saturday, July 15, 2023 8:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Ligand superposition!
Thanks Boaz,
The proteins are all completely different in folds and structures!
Rams
subra...@purdue.edu<mailto:subra...@purdue.edu>
On Jul 1
Thanks Boaz,
The proteins are all completely different in folds and structures!
Rams
subra...@purdue.edu
> On Jul 15, 2023, at 8:04 AM, Boaz Shaanan wrote:
>
> External Email: Use caution with attachments, links, or sharing data
>
> Hi,
> -You may want to send a query to the UCSF
Hi,
-You may want to send a query to the UCSF chimerax/chimera people. They may
suggest how to this using scripts.
- I have not done this on 50 structures, only on few ones. In my experience, if
the proteins are sufficiently similar there is a good chance that superimposing
the proteins will als
On 15/07/2023 03:49, Subramanian, Ramaswamy wrote:
I have over 50 pdb files that I have downloaded from PDB that all have
the same ligand bound.
I wamt to superpose the ligands (and move the protein coordinates
using that matrix). The goal is for me to see how difference in
ligand environmen
