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.
>>>
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>>
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
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