Re: [PyMOL] rotate cell

2013-11-11 Thread Folmer Fredslund
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 Folm

[PyMOL] rotate cell

2013-11-11 Thread Chandan Choudhury
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 achei

Re: [PyMOL] default values in pymol?

2013-11-11 Thread neshat haq
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 wrote: > > > Can

Re: [PyMOL] default values in pymol?

2013-11-11 Thread Thomas Holder
Hi Neshatul, have you looked at AtomInfoAssignParameters in layer2/AtomInfo.c ? Cheers, Thomas On 09 Nov 2013, at 17:17, neshat haq 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 combinations of atoms, like >

Re: [PyMOL] default values in pymol?

2013-11-11 Thread Jason Vertrees
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 wrote: > Can anyone tell where can I get the default values of van der wall

Re: [PyMOL] apply spectrum per MODEL in PyMOL script

2013-11-11 Thread Jason Vertrees
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 wrote: > Hello List, > > is

Re: [PyMOL] Automatic mutation introduction

2013-11-11 Thread White, Mark
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: http://dunbrack.fccc.edu/SCWRL3.php/