Hi Anasuya, > 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. > ZONE1] and then extract another zone, which has complete residues > within 4.5Angstroms of ZONE1, [i.e.ZONE2] I need to store these two > zones in two separate .pdb files. > How can this be done? So far I have managed to extract ZONE1 for all > the PDB ID's and saved their corresponding .pdb files, but, I was > stuck at the next step.
I guess you mean residues that have any atom within 4.5 Angstroms of the ligand? And for ZONE2 residues that have any atom within 9.0 Angstroms of the ligand, but are not already in ZONE1, right? # select first ligand select ligand, byres (first organic) # zone 1 select ZONE1, byres (ligand around 4.5) # zone 2 select ZONE2, byres (ligand around 9.0) and not ZONE1 # save to files save zone1.pdb, ZONE1 save zone2.pdb, ZONE2 Have a look at http://pymolwiki.org/index.php/Selection_Algebra Cheers, Thomas -- Thomas Holder MPI for Developmental Biology ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2 _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
