Dear PyMol Users,
I asked this question but no body replied so I am trying again.
I am struggling here two things.
1). I want to place a pseudo
atom in the charge centre of a non aromatic residue, like arginine.
2). Is it possible to place
a
pseudo
atom in the centre of a cavity in
Linux PyMol v-1.8.4.0
I have installed the LISICA module with no warning or error messages.
Unfortunately qwhen I try to use the plugin I get a 'No module named
License' error.
Here is the entire error message:
Error: 2
Exception in Tk callback
Function: at 0x7f9b800706e0> (type: )
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
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
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,
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
