[PyMOL] Ligand - binding

Hey guys, I was wondering if someone could give me some information, I tried finding it out myself but failed. I just recently started using pymol. What I am trying to achieve: I have a protein (Sequence known), based on experiments I know that it is a creatine transporter. My first problem is tha

Re: [PyMOL] Ligand - binding

Hi Michael, where did you look for creatine? My first stop would be the pdb, and when I type the word creatine in the ligand search window, I get three hits: 3A6J 3B6R 1V7Z Identification of ligand binding sites and computational docking of ligands is a bit more involved than opening both c

[PyMOL] Drawing chain to visualize backbone

Dear all, I have a complex protein (with a knot in the polypeptide chain) and want to show the rough course of the chain, so everyone can easily see that there is a knot inside. I don't know how to draw such a complex 3D object in a drawing program, so I want to do that in PyMol (or another simil

Re: [PyMOL] Drawing chain to visualize backbone

Hi Simon, Maybe this will help. First create a molecule containing only the Calphas: > create calphamol, whatever_your_pdb_name and n. ca then you can delete your original pdb and continue: > set ribbon_trace_atoms, 1 > show ribbon You are breaking your chain because of the amino acid numbering

[PyMOL] alter atom coordinates sequentially

Hi Pymol users, I posted a question last week (attached below) that didn't generate any responses so I'm thinking maybe I was being too specific. So I'd like to restate the problem in a much more general way: I'm trying to apply a set of shifts sequentially from a numpy array to each atom in t

Re: [PyMOL] alter atom coordinates sequentially

Hi Pawel, sorry that you didn't get a reply. Some hints: - it looks like IDs are always reset with "cmd.create", but with "cmd.copy" there are not http://pymolwiki.org/index.php/Copy - "ID" is neither necessarily unique nor contiguous (for example the TER record in a PDB file has it's own ID)

Re: [PyMOL] alter atom coordinates sequentially

Thanks Thomas! That helped greatly. Best, Pawel On 11/14/2013 02:07 PM, Thomas Holder wrote: > Hi Pawel, > > sorry that you didn't get a reply. Some hints: > > - it looks like IDs are always reset with "cmd.create", but with "cmd.copy" > there are not > > http://pymolwiki.org/index.php/Copy > >