[PyMOL] ray-tracing cones

2013-08-19 Thread Bryn Fenwick

Hi All,

I am trying to ray trace an empty cone. I can find no way to get an image of 
the inside of the cone. Does anyone have a work around. Example attached.

run test.py
cone
ray

when the ray command is issued the cone disappears from view.

robert


#
# test.py
#


from pymol import cmd
from pymol.cgo import *


def cone(name='cone'):

o = []

o.extend( [ CONE,
  0.0, 0.0, 0.0,# XYZ 1
  0.0, 0.0, 1.5,# XYZ 2
  0.0,  # Radius 1
  0.3,  # Radius 2
  1.0, 0.0, 0.0,# RGB Color 1
  0.0, 0.0, 1.0,# RGB Color 2
  0.0, 0.0, # Caps 1 & 2
] )


cmd.load_cgo(o, name)

cmd.extend('cone', cone)

-- 
R. Bryn Fenwick,
Structural and Computational Biology,
The Scripps Research Institute,
10550 North Torrey Pines Rd.,
La Jolla, CA 92037, USA.
fenw...@scripps.edu



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[PyMOL] translation without rotation

2009-05-06 Thread R. Bryn Fenwick

Hi,

I am trying to translate some object selections and notice that they  
are undergoing rotations at the same time. I am not sure why this  
occurs. Can anyone suggest a way to stop this from happening? When I  
look at the output I can clearly see that a rotation has also occurred.

my commands look at bit like:

# 1.pdb contains several models
# ref.pdb contains a single structure for a common reference

load ref.pdb
load 1.pdb, 1
load 1.pdb, 2

hide all

select bb, resid 342-381 and name ca+c+n and not ref

show sticks, bb

align 1, ref
align 2, ref

set state -1
set all_states,1

center all

translate [-60.0,0.0,0.0],1
translate [60.0,0.0,0.0], 2


R. Bryn Fenwick


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[PyMOL] export frames as pdb

2010-06-24 Thread R. Bryn Fenwick

Hi,

I have a pdb file that has some models in it. when I open this file  
they are read in as frames, however now I would like to write them out  
as frames in a model file. how can i do that?

Many thanks,

R. Bryn Fenwick


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[PyMOL] ideal beta-sheet

2010-07-21 Thread R. Bryn Fenwick

Hi,

I would like to build an ideal beta-sheet fold. Can anyone suggest how  
to do this with pymol or any other program. I have already tried with  
the build command, however I am not sure how to proceed once the first  
strand is built.

Many thanks,

Bryn





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[PyMOL] pymol

2010-11-03 Thread R. Bryn Fenwick

naming,

Hi,

I have just been looking at the 1.3 build of pymol that comes from  
FINK and see that in the build menu that both residues N and Q have  
the shortcut N.

Bryn


R. Bryn Fenwick



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