Right, forgot to mention that the bin is given as the coordinates of the lower corner, relative to the minimal coordinates.
Cheers, Tsjerk On Thu, Oct 27, 2011 at 6:02 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hey :) > > Does the script pasted below do what you want? It does not move the > molecule(s), but it returns a list of occupied bins with the ids, > names and chains of residues in it. > > Hope it helps, > > Tsjerk > > ### > > from pymol import cmd > > def _bin(x,d): > d = float(d) > a,b,n = min(x),(1-1e-16)/(max(x)-min(x)),int((max(x)-min(x))/d+0.5) > return [ int(b*(i-a)*n)*d for i in x ] > > def bin(sele="all",d=5): > m = cmd.get_model(sele) > b = zip(*[ _bin(i,5) for i in zip(*m.get_coord_list()) ]) > print b > d = dict() > for i,j in zip(b,m.atom): > d[i] = d.get(i,[]) + [(j.resi, j.resn, j.chain)] > return d.items() > > > > > On Thu, Oct 27, 2011 at 4:25 PM, Thomas Holder > <spel...@users.sourceforge.net> wrote: >> 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 >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands ------------------------------------------------------------------------------ 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
