Hi Anasuya, > 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 ones of lesser dimensions? Say, 5A x 5A x 5A?
I'm not aware of any straightforward solution for this. You could write a python script that creates selections for each (sub)cube, but I guess it will be a quite complex script. Have a look at http://pymolwiki.org/index.php/SelInside which should cover all necessary API functions. > Once i generate these smaller cubes, is there a way via pymol, by which i can > navigate through the protein molecule, (smaller)cube by (smaller)cube? > As in, can pymol be used to tell me which residues are lying in which > (smaller) > cube and so on? If you have selections for each cube, try this to lookup cubes that contain atoms of residue number 10: print cmd.get_names('public_selections', 0, 'resi 10') > Can all this be done in a single pymol window/script? > please let me know. > > Thanks > -Anasuya Cheers, Thomas -- Thomas Holder MPI for Developmental Biology ------------------------------------------------------------------------------ The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev _______________________________________________ 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
