[PyMOL] script to write down distances ligand-protein: need feedback

Hi guys, I am trying to make a script to automatize a procedure. I have got a file where I can pick up the structure of protein-ligand complexes cluster The script below read the number of the cluster and then visualize them align with a protein reference. Everything is fine except I'd like write o

Re: [PyMOL] script to write down distances ligand-protein: need feedback

Hi, Well, the cmd.distance method seems to take minimum 4 parameters, not three: cmd.distance( string name, string selection1, string selection2, string cutoff, string mode ) where 'mode' is not important. So, in the script you give, the line: HBA = cmd.distance('(lig and acc)','(active and

RE: [PyMOL] Electron density around selected residues

Akanksha, The carve option to isomesh and isosurface uses a distance-based cutoff for display around the selected atoms. To accomplish what you seek, you should be able to simply reduce that cutoff. Cheers, Warren From: pymol-users-ad...@lists.sourceforge

Re: [PyMOL] script to write down distances ligand-protein: need feedback

> HBA = cmd.distance('HBA', '(lig and acc)','(active and don)', 3.2) yes thanks for the trick. However, I edited my script to: DistOutput.write(" %14s %14s %8s %8s\n"%("donor","acceptor","hba","hbd")) DistOutput.write(" %14s %14s %8.3f %8.3f\n"%(Don,Acc,HBA,HBD)) but I cannot figure out the mea

[PyMOL] rearranging the coordinates of a PDB file

Hi all, I'm a new user of MacPyMOL. I would like to modify the coordinates of my PDB file such that the origin (0,0,0) is centered at the mid-point of a molecular bond. I've found that I can make (and save) changes in the Z and Y coordinates (in 3 button editing mode moving the structure up/

[PyMOL] hardware stereo on window XP

I am a new user of pymol, I have learned a lot from the pymol list. Thank you all. Now I am trying to set up a hardware stereo viewing system on a PC running windows XP. I read the pymol list, and got some idea of installing hardware on window XP system, which is to get a nVidia graphic card FX3200

Re: [PyMOL] script to write down distances ligand-protein: need feedback

Hi, I suppose that these numbers are the atom_ids. It's probably the same numbers returned by the cmd.index function. I guess you could test this by typing "select atom260, id 260" and see if that makes a selection with atom260... As for the speed question, I have no idea. More of a question for

[PyMOL] FPS on FC4 with ATI Mobility Radeio 9700

I have Pymol installed on my dual boot Asus M6Ne notebook and have noticed that the performance is significantly better in windows than it is in linux. I am running FC4 and have installed the ati-fglrx driver. When rotating a 120 amino acid protein I get maximum 8 frames per second and the CPU

Re: [PyMOL] rearranging the coordinates of a PDB file

Hi Vanessa, (1) Are there commands that I can type such that I can shift the coordinate for the entire PDB file without using the mouse? Try: alter_state 1,selection,(x,y,z)=(newx,newy,newz) (2) If the mouse is the only way I can shift coordinates, then how do I use the mouse so that I

[PyMOL] geometric location of amino acids in proteins

Dear All, I would like to know is there any possibility to determine the geometric location of amino acids in proteins using PYMOL. and visualize them.? (or) Please tell emt he softwares to do the same. With regards sankari __ Do You Yahoo!?

[PyMOL] list residues in a selection

Is there a way to list the residues that are in a selection? For example if I use the command "select near, sel01 around 6" how can I obtain a list of the residues in the "near" selection? thanks, Sebastien