On 03/02/2012 11:49 AM, Troels Emtekær Linnet wrote:
How does your execution file look like?
You point to another python to execute the __init__.py file.
You can also define PYTHONPATH or set the PYMOL_PATH
if necessary.
It's MacPyMOL, so this will not work. The _cmd module is compiled into
Hi all,
Can recursive transparency be set on a per-object basis when raytracing
with PyMol? I'm trying the obvious (chB and chA are molecular objects):
set transparency_mode, 2, chB
set transparency_mode, 1, chA
... which PyMol syntaxically accepts, but does not seem to give the
expected
What's going wrong with this code?
___CODE___
from pymol import cmd
def process_line(x):
pdbid,res,chain,num = x.split()
cmd.load(pdbid)
cmd.select(target,(resn %s and chain %s and resi %s)%(res,chain,num))
cmd.select(zone2,(br. (target expand 9 and not (target expand 4.5)) and not
Hey Anasuya,
On Fri, Mar 2, 2012 at 5:13 PM, Anasuya Dighe anas...@mbu.iisc.ernet.in wrote:
What's going wrong with this code?
___CODE___
from pymol import cmd
def process_line(x):
pdbid,res,chain,num = x.split()
cmd.load(pdbid)
cmd.select(target,(resn %s and chain %s and resi
Hi Dominik,
This looks like a bug. We're looking into it.
Cheers,
-- Jason
On Thu, Mar 1, 2012 at 11:35 AM, Dominik G tno...@gmail.com wrote:
Hi pymolers,
I attempt to send a structure from a program to PyMol, which doesn't work.
After some time I've managed to extract the smallest data
Hi Benjamin,
transparency_mode is a global setting and so cannot be applied to
individual objects.
If you'd like to see this as a new feature, please request it:
https://sourceforge.net/tracker/?group_id=4546atid=354546.
Cheers,
-- Jason
On Fri, Mar 2, 2012 at 9:42 AM, Benjamin Bouvier
Hi,
I am running this code on some pdb files: 12gs.pdb, 182l.pdb, 183l.pdb
CODE
from pymol import cmd
def process_line(x):
pdbid,res,chain,num = x.split()
cmd.load(pdbid)
cmd.select(target,(resn %s and chain %s and resi %s)%(res,chain,num))
cmd.select(zone2,(br. (target expand 9 and
Dear Colleagues,
This is a reminder that the deadline for applications for the 5th annual CCP4
Summer School From data collection to structure refinement and beyond is
April 17, 2012. The school will take place from June 19 through June 26, 2012
at the Advanced Photon Source (APS) near
Hi Anasuya,
your pdbid variable actually holds the file name (including
extension), so the delete statement fails.
Fix it like this:
cmd.delete(pdbid.split('.')[0])
Cheers,
Thomas
Anasuya Dighe wrote, On 03/02/12 19:38:
Hi,
I am running this code on some pdb files: 12gs.pdb, 182l.pdb,
