Re: [PyMOL] Pseudoatom for a cavity

​Hey Tsjerk!
So good to connect again here!
​I will look up Mole plugin for possible channels, come back and write here
again and a script would of course be very nice to have.

Thanks for the help.
Kanika

On Thu, Jan 26, 2017 at 10:39 PM, Tsjerk Wassenaar <ts...@gm...>
wrote:

> 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
>>
>> Work: +1 301 846 5993 <(301)%20846-5993>
>> Mob.: +1 240 367 5208 <(240)%20367-5208>
>> Website: http://www.hiteshpatel379.com/
>> Email: hit...@ni...
>>
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>


-- 
*Best,*

*Kanika Sharma*