Oh, pymol.finish_launching() was missing, I feel so terrible now. Thanks a lot for your help.
Regards. On Thu, Apr 6, 2017 at 4:36 PM, Thomas Holder <thomas.hol...@schrodinger.com> wrote: > Hi Ahmad, > > I assume you don't launch PyMOL properly, please read > https://pymolwiki.org/index.php/Launching_From_a_Script > > Cheers, > Thomas > > On 06 Apr 2017, at 16:01, Ahmad Abdelzaher <underoath...@gmail.com> wrote: > >> I did remove it. I get the same error. >> >> Regards. >> >> On Thu, Apr 6, 2017 at 3:59 PM, Jed Goldstone <jedg...@gmail.com> wrote: >> centerofmass 1a5m >> works just fine for me from the console. >> Try removing the ".pdb" from the command >> "com = cmd.centerofmass('1a5m.pdb')" >> >> Jed >> >> On 4/6/2017 9:36 AM, Ahmad Abdelzaher wrote: >> I don't fully get what you mean, however, with or without the .pdb, I >> get the same error. >> >> On Thu, Apr 6, 2017 at 3:28 PM, João M. Damas <jmda...@itqb.unl.pt >> <mailto:jmda...@itqb.unl.pt>> wrote: >> >> When you do the load, the .pdb is stripped off. The selection is >> 1a5m and not 1a5m.pdb >> >> On Thu, Apr 6, 2017 at 3:18 PM, Ahmad Abdelzaher >> <underoath...@gmail.com <mailto:underoath...@gmail.com>> wrote: >> >> In the documentation, it said "atom selection. However i tried >> the following as you suggested: >> >> import __main__ >> __main__.pymol_argv = ['pymol','-qc'] >> import pymol >> from pymol import cmd >> >> cmd.delete('all') >> cmd.load('1a5m.pdb') >> com = cmd.centerofmass('1a5m.pdb') >> print(com) >> >> I received the following: >> >> File >> "C:\Users\Ahmad\Anaconda3\lib\site-packages\pymol\querying.py", >> line 1674, in centerofmass >> states = [get_selection_state(selection)] >> >> File >> "C:\Users\Ahmad\Anaconda3\lib\site-packages\pymol\querying.py", >> line 1641, in get_selection_state >> _self.get_object_list('(' + selection + ')'))) >> >> TypeError: 'NoneType' object is not iterable >> >> On Thu, Apr 6, 2017 at 1:09 PM, David Hall >> <li...@cowsandmilk.net <mailto:li...@cowsandmilk.net>> wrote: >> >> >how to calculate the center of mass of an entire structure >> >> Let's say I want the center of mas of the structure from the >> PDB 1vdd >> >> cmd.fetch('1vdd', async=0) >> >> cmd.centerofmass('1vdd') >> >> Now, I see 1vdd has a bunch of water molecules that I don't >> want in in my calculation >> >> cmd.centerofmass('1vdd and not solvent') >> >> Now maybe I only care about chain A. >> >> cmd.centerofmass('1vdd and not solvent and chain A') >> >> I suggest reading more about selections in the pymolwiki. >> That is actually a topic where I feel the wiki could be >> better organized, but almost every command in pymol operates >> on selections, so it is a fundamental concept you should >> spend time to understand if you are planning to use pymol. >> >> https://pymolwiki.org/index.php/Category:Selecting >> <https://pymolwiki.org/index.php/Category:Selecting> >> >> >> On Thu, Apr 6, 2017 at 1:13 AM, Ahmad Abdelzaher >> <underoath...@gmail.com <mailto:underoath...@gmail.com>> wrote: >> >> Hi Tsjerk, >> >> What you said makes perfect sense. Since an atom could >> be considered as a point with uniform density, it's >> center of mass is indeed its position. >> >> Which, begs the question, what is the purpose of >> cmd.centerofmass() and how to calculate the center of >> mass of an entire structure (the only calculation that >> would make sense with regards to the center of mass). >> >> Cheers. >> >> >> On Thu, Apr 6, 2017 at 6:49 AM, Tsjerk Wassenaar >> <tsje...@gmail.com <mailto:tsje...@gmail.com>> wrote: >> >> Hi Ahmad, >> >> The center of mass of an atom is its position. A >> function like cmd.centerofmass in the context of >> pymol only makes sense with a selection. E.g.: >> >> x,y,z = cmd.centerofmass('byres n. ca') >> print "COM of protein:", x, y, z >> >> Hope it helps, >> >> Tsjerk >> >> On Thu, Apr 6, 2017 at 6:30 AM, Ahmad Abdelzaher >> <underoath...@gmail.com >> <mailto:underoath...@gmail.com>> wrote: >> >> Well I'm assuming the selection goes in the >> argument of cmd.centerofmass(), however, does it >> have to be an atom? How should I calculate the >> center of mass for an entire protein? >> >> On Thu, Apr 6, 2017 at 4:48 AM, David Hall >> <li...@cowsandmilk.net >> <mailto:li...@cowsandmilk.net>> wrote: >> >> It returns the x, y, and z coordinates of >> the center of mass as a list of 3 floats, >> presumably in that order? >> >> Is there another question? The page >> describes the arguments and their defaults >> so I am unsure what is lacking. >> >> -David >> >> On Apr 5, 2017, at 10:29 PM, Ahmad >> Abdelzaher <underoath...@gmail.com >> <mailto:underoath...@gmail.com>> wrote: >> >> I find the documentation about the python >> api here to be a bit lacking. >> >> https://pymolwiki.org/index.php/Centerofmass >> <https://pymolwiki.org/index.php/Centerofmass> >> >> I would appreciate more info on how to use >> this: cmd.centerofmass() returns a list of >> 3 floats. >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> >> -- >> João M. Damas >> PhD Student >> Protein Modelling Group >> ITQB-UNL, Oeiras, Portugal >> Tel:+351-214469613 > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ 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
