Hi James, the "get_extent" command in PyMOL will give you the corners of the selected region, from which you easily can calculate center and edge lengths.
http://pymolwiki.org/index.php/Get_extent Example: box = cmd.get_extent('sele') print 'Center:', [(a+b)/2.0 for (a,b) in zip(*box)] print 'Size:', [(b-a) for (a,b) in zip(*box)] Regarding your issue (1-): Coordinates should not change unless you align to some other molecule. Cheers, Thomas On 07/18/2012 09:37 AM, James Starlight wrote: > Jordan, > > Thank you for advise. > > I've tried to do the same already but > > 1- In Resulted pbd file ( with ligand and surrounded residues only) > the coordinates of ligand and residues have been changed in > comparison to the initial pdb/ How to prevent it? > > 2- The resulted pdb consist of coordinates of each atoms but how to > define the proper coordinates of ligand-binding BOX based on that > point coordinates? > > James > > 2012/7/18 Jordan Willis <jwillis0...@gmail.com>: >> I'm thinking a good work around is simply this. >> >> >> Select the binding site of the amino acids and ligand in pymol. >> >> Then copy those selected aa's and atoms to another object: >> save -> model -> copied_object as output.pdb >> >> output.pdb will then contain all the x,y,z coordinates of only what was >> selected. >> >> Then just get those columns and upload them to swiss dock. >> >> Jordan >> >> >> On Jul 18, 2012, at 2:23 AM, James Starlight wrote: >> >>> Dear PyMol users! >>> >>> >>> Some of docking servers (e.g swiss dock) which I'm using need in >>> explicit definition of the coordinates (in XYZ) of the docking region >>> as well as coordinates of its COM. How I could obtain such coordinates >>> of intrested pdb file based on the knowing protein-ligand interaction >>> sites ( e.g if i visualize ligand binding site by means of Pymol >>> itself ). >>> >>> >>> Thx for help >>> >>> >>> James -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ 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
