In addition I'd like to know more about possible flexibility in the
representation of the protein-ligand contacts by means of the present->
ligand site option.
For instance sometimes I have ligand group situated in the some distance
from the interiour group. So this space forms empty cavity around
Hi James,
> I have no problems with the representation of the assigned ligand with
> its environment but when I save this as new pdb via
>
> save test.pdb, visible
>
> my output pdb contains some errors like missing bonds between HETATM
> residues ( ligand ) etc.
maybe this trick was too dirty...
Thomas, thanks again!
I want to recall to the ligand assignment via
select motif, (pepseq TYG) and not (name C+N+O)
alter motif, type="HETATM"
I have no problems with the representation of the assigned ligand with its
environment but when I save this as new pdb via
save test.pdb, visible
m
Hi James,
> How I could select all this visible (relevant) part and save it in the
> separate pdb?
> I've not found such simple selection by the visible part in the
> selection algebra :(
use the "visible" single-word selector :)
http://pymolwiki.org/index.php/Single-word_Selectors
save onlyvis
Thanks Thomas
I've just one extra question about ligand sites.
As I've said previously I can obtain information about polar contacts
between ligand and its surrounding residues via Present- ligand sites.
On the next step I mask all other non relevant parts of the protein ( wich
are represented a
Hi James,
> 1- Some of my proteins consist of ligand wich include some of amino
> acids from sequence of my protein ( e.g fluorophores in GFP). So I'd
> like to assign some residue motif as the ligand group ( e.g Ser Tyr Gly
> motif in GFP). How I could do it?
The preset selects hetatoms as ligan
