Nat,
Thanks for this -- it's always good to expand the PyMOLWiki to new
applications for PyMOL.
Cheers,
-- Jason
On Mon, Jan 23, 2012 at 2:08 PM, Nat Echols wrote:
> On Mon, Jan 23, 2012 at 12:42 PM, Simon Becker
> wrote:
>> I would like to visualize the intermediate structures my program
>>
On Mon, Jan 23, 2012 at 12:42 PM, Simon Becker
wrote:
> I would like to visualize the intermediate structures my program
> produces during the computation cycle. Every iteration it generates a
> new structure. Is there a way to display this structure in pymol, using
> e.g. a pipe? Does anyone have
On Mon, Jan 23, 2012 at 12:42 PM, Simon Becker
wrote:
> I would like to visualize the intermediate structures my program
> produces during the computation cycle. Every iteration it generates a
> new structure. Is there a way to display this structure in pymol, using
> e.g. a pipe? Does anyone have
Hi all,
I would like to visualize the intermediate structures my program
produces during the computation cycle. Every iteration it generates a
new structure. Is there a way to display this structure in pymol, using
e.g. a pipe? Does anyone have experience with this, is there even a
tutorial or
Hi James,
the selection makes the flexibility:
# Example: non-polar residue carbons
remove hydro
h_add (resn ILE+LEU+VAL+MET) and (elem C)
# Example: polar but not backbone
remove hydro
h_add (acceptors or donors) and not (name N+O)
Also bond order and formal_charge determine where to add a hyd
Dear PyMol users!
I have one extra question about addition of the missing Hydrogen atoms to
my structure.
I've found that I could do it via context Hydrogen command as well as via
H_add command.
Now I want to add only specific hydrogens to the specific residues of my
proteins ( e.g only alympha
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
