Right, forgot to mention that the bin is given as the coordinates of
the lower corner, relative to the minimal coordinates.
On Thu, Oct 27, 2011 at 6:02 PM, Tsjerk Wassenaar <tsjerkw@...> 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,
> 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
> <speleo3@...> 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.
>> 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@... Self-Assessment and learn
>> about Cisco certifications, training, and career opportunities.
>> PyMOL-users mailing list (PyMOL-users@...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@...>
> 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.
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen