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> 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
>
>
> On Thu, Apr 6, 2017 at 1:13 AM, Ahmad Abdelzaher <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>
>> 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
>>> > 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>
>>>> 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>
>>>>> wrote:
>>>>>
>>>>> I find the documentation about the python api here to be a bit
>>>>> lacking.
>>>>>
>>>>> https://pymolwiki.org/index.php/Centerofmass
>>>>>
>>>>> I would appreciate more info on how to use this: cmd.centerofmass()
>>>>> returns a list of 3 floats.
>>>>>
>>>>> ------------------------------------------------------------
>>>>> ------------------
>>>>> 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
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>>>>> t
>>>>>
>>>>>
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
>>>> Check out the vibrant tech community on one of the world's most
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>>>> _______________________________________________
>>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
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>>>>
>>>
>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>>
>>>
>>
>
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