Hi Jordan et al., Yes one can use the alter command with a whole selection at once and it is much faster. I hadn't realized that until Thomas Holder helped fix my script that appears to do what you were wanting to do:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/data2bfactor.py The B-factor data is read in and assigned to a dictionary by the "atom_data_extract" function elsewhere in the script (indexed either by chain and residue number, or by chain and ID) and then it is applied like this: b_dict = atom_data_extract(data_file) quiet = int(quiet) == 1 def b_lookup(chain, resi, name, ID, b): def _lookup(chain, resi, name, ID): if resi in b_dict[chain] and isinstance(b_dict[chain][resi], dict): return b_dict[chain][resi][name][0] else: # find data by ID return b_dict[chain][int(ID)][0] try: if not chain in b_dict: chain = '' b = _lookup(chain, resi, name, ID) if not quiet: print '///%s/%s/%s new: %f' % (chain, resi, name, b) except KeyError: if not quiet: print '///%s/%s/%s keeping: %f' % (chain, resi, name, b) return b stored.b = b_lookup cmd.alter(mol, '%s=stored.b(chain, resi, name, ID, %s)' % (prop, prop)) cmd.rebuild() Hope that helps. Cheers, Rob On Tue, 2015-06-16 11:10 EDT, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Jordan, > > The answer is something like (assuming reading from a file): > > newb=[float(i) for i in open("stuff.dat").read().split()] > alter n. ca, b=newb.pop() > spectrum b > > Hope it helps, > > Tsjerk > > On Tue, Jun 16, 2015 at 10:25 AM, Jordan Willis > <jwillis0...@gmail.com> wrote: > > > Hi Tsjerk, > > > > It seems everyone is pointing to this ( > > http://www.pymolwiki.org/index.php/Color#Reassigning_B-Factors_and_Coloring) > > which I somehow missed. However, they seem to be altering one > > residue at a time like I’m doing. > > > > > > Jordan > > > > On Jun 15, 2015, at 11:59 PM, Tsjerk Wassenaar <tsje...@gmail.com> > > wrote: > > > > Hi Jordan, > > > > Yes, although I don't have the answer at hand, it has been given on > > the user list several times. You can find it in the archives. > > > > Cheers, > > > > Tsjerk > > On Jun 16, 2015 08:16, "Jordan Willis" <jwillis0...@gmail.com> > > wrote: > > > >> Hi, > >> > >> I have a dictionary that has a bunch of values I want to assign to > >> b-factors in order to color by. In my script: > >> > >> for residue in data: > >> cmd.alter(“resi > >> {}”.format(residue[‘resnum’]),”b={}”.format(residue[‘value’])) > >> > >> This executes the alter command for each residue. For some reason, > >> its taking forever in my script. Is there something inherently > >> inefficient about alter? And is there anyway to fix it? Perhaps, > >> assign a bunch of b-factors at once. > >> > >> Jordan > >> > >> > >> ------------------------------------------------------------------------------ > >> > >> _______________________________________________ > >> 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 > >> > > > > > > -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc ------------------------------------------------------------------------------ _______________________________________________ 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
