Hi Jacob,
The following command will make blue to purple spectrum.
(please type in one line)
for i in range(1 + cmd.count_states()): cmd.set("cartoon_color",
"0x%02x00ff" % (i * 255 / (2 + cmd.count_states())), "all", state=i)
You can change spectrum by changing
"0x%02x00ff" % (i * 255 / (
Hey :)
You could copy the state to the b-factor field:
fetch 1nmr, async=1
split_states 1nmr
for i in range(1,cmd.count_states()+1): cmd.alter("1nmr_%04d"%i,"b=%d"%i)
delete 1nmr
spectrum b
Cheers,
Tsjerk
On Mon, Dec 19, 2011 at 7:38 AM, Jason Vertrees
wrote:
> Hi Jacob,
>
> You cannot use th
Hi Jacob,
You cannot use the spectrum command across multiple states like that.
Your next best bet is to try:
set color, color_name, obj_name, state=X
For example,
set line_color, red, myProtein, state=1
set line_color, orange, myProtein, state=2
set line_color, yellow, myProtein, state=3
...
Dear Pymol list,
I have been trying to color the states in a morph by spectrum to try
to show the motion in still form, using the following method:
split_states foo, # after which I get the states as new objects as expected
color_obj(rainbow=1) # after which I get the following error mess
Hi Arne,
PyMOL can read various cube-type files. Find the common format between
Gaussian and PyMOL and use that one. After it's loaded into PyMOL you
can represent the data as isomesh, isocontour, slice, gradient, and
volume.
Cheers,
-- Jason
On Sun, Dec 18, 2011 at 3:38 PM, Arne Dieckmann wro
Dear all,
how would I render molecular orbitals in pymol? I thought about exporting a
cube-file from Gaussian containing a specific MO and importing this into pymol.
Is that possible? If not, how would I do this? Thanks a lot!
Cheers,
Arne
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