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