[PyMOL] Coloring c-alpha atoms makes cartoons colored too

Hi everyone, I want to color C-alpha atoms of a selection in a specified colour (red) and and the cartoon representation in a separate color(grey). When i try colouring the calpha's in red, the same color leaks onto to the cartoon representation also, making it look grey with patches of red. Ha

[PyMOL] How to make outlines to spheres drawn in PyMOL ?

Dear users, I was interested in knowing if there is an option or setting in PyMOL which is able to make an outline to spheres. I am aware of the show spheres command and have used it extensively to show C-alpha atoms of amino acids as spheres. I am curious to know how I could make an outline to

[PyMOL] using pymol commands in a script

Hi everyone, How to write PyMol commands in Python script, save a session and then save a .png file of the same ? I have an input file which has the protein information i.e name, chain, and a list of residues. I want to plot the C-alpha atoms of these residues for each protein & calculate distance

[PyMOL] Making selections separately among 2 or more proteins loaded into PyMOL

ng 3 different chains among 3 separate proteins ? Will the align command suffice ? Please let me know. Thanks & Regards, Anasuya Dighe Molecular Biophysics Unit Annexe, Indian Institute of Science, Bangalore - 560012 INDIA -- This message has been scanned for viruses and dangerous co

[PyMOL] Splitting a PDB file into its constituent chains, and making multiple (smaller) PDB files

, 1a55_Q.pdb, 1a55_R.pdb Also, in case I have a large number of multiple chain PDB files, how could I go about splitting each of them? Please help. - Anasuya Dighe -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean

[PyMOL] About draw_links.py by Dr. Robert Campbell

his using draw_links.py? Where am I going wrong? - Anasuya Dighe -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Everyone hates slow websites. So do we.

[PyMOL] About ray trace and spheres

Hi, I am representing C-alpha atoms of binding site as spheres. I am using the set sphere_mode command to adjust the radius of the spheres. I use the sphere_mode as 4. However, when I do a ray tracing, no matter how small the spheres I set, they appear very large once the ray tracing is carried ou

[PyMOL] selecting atoms around a ligand in a protein structure

Hi Pymol-users, I need to select only the atoms [and NOT complete amino acid residues] which are lying in a radius of 4.5 Angstroms from the ligand from a ligand-bound protein structure. I am aware that the command: select site, br. resn FAD and chain A and resi 45 around 4.5 and not HETselect

[PyMOL] Having problem running: findSurfaceResidues.py

Hi Pymol Users, I was trying to use the findSurfaceResidues.py script listed on PyMOLwiki (http://www.pymolwiki.org/index.php/FindSurfaceResidues), to find out which residues which are present on the surface of the protein. These are the steps I have followed: 1) Made a file called findSurfaceRes

[PyMOL] FInd the number of residues within a selection

Hello, I wanted to know what is the command-line syntax for finding out the number of residues which fall within a selection made in PyMOL. Once the selection is made, the command line shows the number of atoms selected, but I wanted to know the number of residues present in such subsequent selec

[PyMOL] Creating dummy zones

Hi, I have around 18000 ligand-bound PDB's. I have as of now, extracted zones of amino acid residues (say ZONE-1) which are within a radius of 4.5A from the ligand, for each of the (18000) ligand-bound PDBs with me. How do I now go about generating, similar RANDOM zones of amino acid residues occur

[PyMOL] multiple occupancies

Hi, I am running this code on some pdb files: 12gs.pdb, 182l.pdb, 183l.pdb CODE from pymol import cmd def process_line(x): pdbid,res,chain,num = x.split() cmd.load(pdbid) cmd.select("target","(resn %s and chain %s and resi %s)"%(res,chain,num)) cmd.select("zone2","(br. (target expand

[PyMOL] what's wrong in this code.. please help!

What's going wrong with this code? ___CODE___ from pymol import cmd def process_line(x): pdbid,res,chain,num = x.split() cmd.load(pdbid) cmd.select("target","(resn %s and chain %s and resi %s)"%(res,chain,num)) cmd.select("zone2","(br. (target expand 9 and not (target expand 4.5)) and

[PyMOL] finding complete residues within a RANGE OF distance cutoff

Hello , I want to extract out complete amino acid residues which fall "within a radius of 4 to 9 Angstroms from the ligand". What do I do in such a case, given the pdb id's, chain ID, the name of the ligand and its residue id? PS: I want to avoid, extracting out cmplete residues within a 0-4.5A

[PyMOL] Putting a protein molecule into a grid and traversing through the grid

how do i put a protein molecule inside a cube with x-axis spanning till the largest x-coordinate, y-axis spanning till the largest y-coordinate, and z-axis spanning till the largest z-coordinate? Once i do this, can i divide the larger cube(i.e. the one holding the entire protein) into smaller one

[PyMOL] Automating pymol through PERL

Hello, I have a .txt file which has data in the following fashion: 19gs BSP A 1 1a2d PYX A 117 9rsa ADU A 125 7kme PRR J 382 1a0r ACE B 1 1a0r FAR G 72 . . . Fields: In such a way, I have data of ar

[PyMOL] help needed

hi all, I am writing this email with regards to the following problem. Statement of the problem: I have around 19,200 unique PDB files. Each of them have one or more ligands in it. For each ligand, I have to extract a zone which contains complete residues within 4.5Angstroms of the ligand [ i.e.