Re: [PyMOL] Pseudoatom for a cavity

[Tsjerk W. <ts...@gm...>]

Hi Kanika,

That's been quite a while! Nice to see you again and to see you're still
your determined self, still a bit impatient, reposting a message within a
day :)

The issue with the second question is not about center_of_mass, but about
center_of_no_mass, which is a bit harder (and I don't think there's an
import for that). You can have a look at hollow.sourceforge.net or so. If
they're channels, connected to the surface of the protein, you can also
have a look at the Mole plugin on the Pymol wiki. Alternatively, I have
some bits of code that could be forged together to get something similar
and which would allow for getting a center_of_no_mass, but I probably won't
be able to do the forging before next week.

Hope it helps,

Tsjerk

On Thu, Jan 26, 2017 at 10:14 PM, Hitesh Patel <hit...@gm...>
wrote:

> Hi,
>
> For your 2nd question:
> You can make pseudoatom at Center of mass or center of geometry (for an
> object or probably selection too) using the following script:
> https://pymolwiki.org/index.php/Center_of_mass
>
> In your case you mat try:
>
> import center_of_mass
>
> com SelectionObjectName, state=1#Create a pseudoatom representing the Object COG and store it as "SelectionObjectName_COM"
>
>
>
> On Thu, Jan 26, 2017 at 4:52 AM kanika sharma <ksh...@gm...>
> wrote:
>
>> Dear PyMol Users,
>>
>> I am struggling here two things.
>> 1). I want to place a pseudoatom in the charge centre of a non aromatic
>> residue, like arginine.
>> 2). Is it possible to place another pseudoatom in the centre of a cavity
>> in the protein? I am thinking how can I define the co ordinates of the
>> position where I wan t to place the pseudoatom?
>>
>> ​Thanks ​
>>
>> --
>> *Best,*
>>
>> *Kanika*
>>
>>
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> --
> Regards,
>
> Dr. Hitesh Patel
> Post-Doctoral Fellow,
> CADD Group,
> Building 376, Room: 205A
> Chemical Biology laboratory,
> Center for Cancer Research,
> National Cancer Institute,
> Frederick, MD-21702
>
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-- 
Tsjerk A. Wassenaar, Ph.D.