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
wrote:
> Hi Kanika,
>
> That's been qui
Is there a way to calculate COM for a tunnel?
On Thu, Jan 26, 2017 at 10:14 PM, Hitesh Patel
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/i
Thanks Jared.
First part, is perfect. So pseudo atom lies between nitrogen atoms.
Second part, I don't have specific xyz coordinates because it is centre of
a tunnel in the protein and that's the struggle.
On Thu, Jan 26, 2017 at 10:01 PM, Sampson, Jared M. <
jms2...@cumc.columbia.edu> 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 thin
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
Hi Kanika -
You can get more information on the wiki:
https://pymolwiki.org/index.php/Pseudoatom.
To answer your specific questions, to make a pseudoatom between the two
terminal Ns of Arg 100 on chain A of myobj:
```
pseudoatom my_ps1, myobj and chain A and resi 100 and name NH1+NH2
```
and
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
positio
