Re: [PyMOL] [EXTERNAL] extract interference residue

klahoma City, OK 73104-5419 > Office: 405-271-8300 Lab: 405-271-8312 > > Websites: > Faculty page: > https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd > BSC-OKC > <https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phdBSC-OKC> > (LBS

[PyMOL] extract interference residue

Hello Guys, I am trying to extract the interference residue from a given protein PDB. I have a protein named 1ak4 which has two chain A and B. I open pymol, then go to file, the run the script from here https://pymolwiki.org/index.php/InterfaceResidues#Simple_Example Then I run the following

Re: [PyMOL] Color change of different domain

y > > > > > > Regards > > > > John > > > > *From:* Mohammad Goodarzi [mailto:mohammad.goda...@gmail.com] > *Sent:* 08 August 2018 16:13 > *To:* pymol-users@lists.sourceforge.net > *Subject:* [PyMOL] Color change of different domain >

[PyMOL] Color change of different domain

I have a protein in PDB called "3E9D" I first get the seqeuence then I go here https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi and I find the domains. Now I am trying to change the color accordingly Now I am trying to change the color of each domain with different color first I change the

Re: [PyMOL] causing to miss atoms

> Kevin Jude, PhD > Structural Biology Research Specialist, Garcia Lab > Howard Hughes Medical Institute > Stanford University School of Medicine > Beckman B177, 279 Campus Drive, Stanford CA 94305 > Phone: (650) 723-6431 > > On Wed, Aug 1, 2018 at 8:03 AM Mohammad Goodarzi

[PyMOL] causing to miss atoms

Hello, I have a protein that i get from PDB https://www.rcsb.org/structure/2J3S then I try to remove the chain B, and all water etc except the chain A. it causes that I miss some atoms on the SER. Can you please advise how to deal with it? Thanks Mohammad

[PyMOL] check structures

Hello, I would like to know how to check for missing or broken part of a PDB file using pymol? should i screen within each amino acid or there is a way to show it by pymol? Thanks Mohammad -- Check out the vibrant tech

[PyMOL] Figures

Hello, How can one plot specific mutation of TP53? I want to show the differences Thanks -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org!

[PyMOL] how to generate random sequences for gromacs

Hi , I am trying to generate random sequences for a given region in order to run Gromacs This is the sequence of my protein MEEKLKKTKIIFVVGGPGSGKGTQCEKIVQKYGYTHLSTGDLLRSEVSSGSARGKKLSEI MEKGQLVPLETVLDMLRDAMVAKVNTSKGFLIDGYPREVQQGEEFERRIGQPTLLLYVDA

Re: [PyMOL] highlight a domain with another color

Mohammad - > > If you know the residue numbers at the domain boundaries, you can do this > at the command line with, e.g.: > > color red, chain A and resi 1-100 > color cyan, chain A and resi 101-200 > etc. > > Hope that helps. > > Cheers, > Jared > > >

[PyMOL] highlight a domain with another color

Hello, I have a sequence and I obtain various domains. I want to show them with various colors. How can one do that? for example can one of you show it on SIRT1 Thanks Mohammad -- Check out the vibrant tech community on

Re: [PyMOL] How to identify the pocket of a protein?

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.co

[PyMOL] How to identify the pocket of a protein?

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 -- Check out the

[PyMOL] Removing unwanted molecules

Hello, I want to know how to delete chain B and all ligands except the one that I want ? Is there any way to know all molecules which comes with a PDB and then remove those that you dont want? Thanks Mohammad