James,
What you want is something like SCWRL from the Dunbrack Lab. Minimization will
not get a sc out of an incorrect rotomer, and will not repack the protein in
the case of multiple mutations, SCWRL will. It can be downloaded for academic
use from here:
Hi Jerome,
fetch 1nmr, discrete=1, async=0
as ribbon
set all_states
for x in range(cmd.count_states()): cmd.color(str(x), state %s % x)
You can substitute the spectrum command for the color command.
Cheers,
--- Jason
On Sat, Nov 9, 2013 at 8:54 PM, Jerome BENOIT g62993...@rezozer.net wrote:
Hi Neshatul,
# print out the vdw values used for a given selection
iterate my_selection, vdw
Use alter to change the values:
alter my_selection, vdw=vdw+2.0
Cheers,
--Jason
On Sat, Nov 9, 2013 at 4:17 PM, neshat haq neshat...@gmail.com wrote:
Can anyone tell where can I get the default
Hi Neshatul,
have you looked at AtomInfoAssignParameters in layer2/AtomInfo.c ?
Cheers,
Thomas
On 09 Nov 2013, at 17:17, neshat haq neshat...@gmail.com wrote:
Can anyone tell where can I get the default values of van der wall radii (or
other radii) used in pymol, for atoms and
Thanks its there in layer2/AtomInfo.c
On Tue, Nov 12, 2013 at 12:16 AM, Thomas Holder
spel...@users.sourceforge.net wrote:
Hi Neshatul,
have you looked at AtomInfoAssignParameters in layer2/AtomInfo.c ?
Cheers,
Thomas
On 09 Nov 2013, at 17:17, neshat haq neshat...@gmail.com wrote:
Dear PyMOL users,
I want to rotate/revolve the loaded structure. The cell parameter should
also rotate.
I am aware of rotate command.
eg. rotate X, 90.
But when I view the cell. The rotation does not happen here.
My purpose is to generated a snapshot showing the boundaries.
How can this be
Dear Chandan,
I think you want to use the move command (
http://pymolwiki.org/index.php/Move) which moves the camera around the
molecule, instead of the rotate command (
http://pymolwiki.org/index.php/Rotate) which alters the coordinates of the
object you are looking at.
Hope this helps
Folmer
