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.
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