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> 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>
> 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> 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
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>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>>>>>>> mol-us...@lists.sourceforge.net
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------
>>>>>> ------------------
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>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Tsjerk A. Wassenaar, Ph.D.
>>>>>
>>>>>
>>>>
>>>
>>
>> ------------------------------------------------------------
>> ------------------
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>>
>
>
>
> --
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
>
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