Hi there,
I have bunch of structures in the session but only one of them (molA)
displayed.
I'm trying to select atoms within a given radius from my point of interest.
When I do
select cont,(/molA//s/401 around 4)
it sure selects all atoms from molA that are within 4 A from residue 401 but
it also
SD is a file format for small molecule ligands based around the MDL MOL file
(CTAB core).
http://www.mdli.com/downloads/literature/ctfile.pdf
Advantages:
simplicity
easy to parse
supported by most cheminformatics packages
captures valence, stereochem, charge
On Thu, 6 Feb 2003, Warren L. DeLano wrote:
> Read-in performace would be better if you could convert your
> multiligand PDB file to an SD file.
Sorry, what's SD?
TIA,
Cheers,
---
Alan Wilter S. da Silva
---
Laboratório de Física Biológica
Instituto de
On Thu, 6 Feb 2003, Chris wrote:
> A couple of quick questions for anyone running Pymol and Autodock.
> 1. Doing Get dockings in autodock writes out a PDB formatted file, and uses
> the ` MODEL ' and ` ENDMDL ' records to denote the different dockings is
> there anyway to get pymol to read these
Oooops
I [2003-02-05 11:42] wrote:
>
> I typically use the following script (I call it make_pov.py) and
> "run" it from pymol once to load the function, and then I do
> "make_pov('povray.inp')" to create the povray.inp file.
But of course I forgot to include the script, which is very short
Hi Guys
A couple of quick questions for anyone running Pymol and Autodock.
1. Doing Get dockings in autodock writes out a PDB formatted file, and uses
the ` MODEL ' and ` ENDMDL ' records to denote the different dockings is
there anyway to get pymol to read these as individual "states" ? - If not
Dear Matt,
There is a straighter way to do it. Try just
pymol.com pymol_script.pml
(This works at least on my Linux machine).
You can also try
cat pymol_script.pml | pymol.com -p
or even
tail -f pymol_script.pml | pymol.com -p
The latter allows one to append lines to the pymol script from a
