> I wonder if there’s any way to get around this? Obviously I can just turn
> off cartoon_side_chain_helper, but it’s so handy...
Jared,
Just select the atoms you want shown as sticks in the side-chain and
turn off their cartoon representation:
# 1. Using the mouse, select just those three oxy
When visualizing a protein, Pymol automatically connects the various atoms.
Is there a method to access the connection graph in a pymol plug-in? What
I want to do, is to write a plug-in so that I click on an atom and have it
create 2 selections, one selection will have all atoms that are connecte
Hi,
I have some ligand files in mol2 format. For each one I have another
file which contains for each atom electrostatic and vdw interaction
information like:
(es) (vdw)
1-0.345 5.413
2 0.653 -0.12
...
What I would like to do is the following:
1- load the mol2 file i
Hi,
I load a ligand file in pymol for visualization. Then I save it to disk,
modifiy it with some quantum program, and after some minutes, when the
calculation ends, I go to pymol (already opened session) and tell pymol
to open the generated file.
For making this procedure faster and more auto
Dear All,
I want to create molecule in Pymol by combining 3 different pdbs.
Two of them are form the pdb data bank and one was created via pymol.
I have the 3 of them open in pymol but now I am trying to figure out
how to connect the termini of the polypeptides in pymol.
I searched the wiki/manua
On Fri, Mar 26, 2010 at 5:14 PM, Werner Schroedinger <
werner.schroedin...@googlemail.com> wrote:
> For making this procedure faster and more automaticm I wonder if somehow
> can I tell pymol to pay atention to some external file, or for the
> ligand being visualized now, to its copy on the hard d
Hi Afonso,
If you want to connect one object to another, you want to check out
the fuse command (help fuse)
fuse atom_to_be_connected_from_object1, atom_to_be_connected_from_object2
Hope it helps,
Tsjerk
On Sun, Mar 28, 2010 at 4:33 PM, Afonso Duarte wrote:
> Dear All,
>
> I want to create mo
Brett,
What exactly do you mean one side vs the other? What separates a
"side"? Regardless, you can achieve what you want in two ways: you
can use PyMOL selections; or you can get a chempy model of your
object. Here is an example for each:
#1 -- get atoms bound to a given "sele" atom:
select v
