D'uh!!!
I need to get used to always ray before assuming anything.
Sorry for the noise!
-Original Message-
From: Justin Lecher [mailto:j.lec...@fz-juelich.de]
Sent: Tuesday, August 26, 2014 4:24 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] cartoon_transparency issue
On 25/08/14 18:42, Markus Heller wrote:
Hello,
Attached is a crop of a figure create with the latest PyMOL under Windoze 7
64 bit. When setting cartoon_transparency, I get a gray band on the
cartoons. Where does this come from, and how do I get rid of it?
Thanks and Cheers
Markus
Here's my code:
# reset everything
delete all
# white background
bg_color white
# show valences
set valence, 1
# show valences inside rings, 0 = centered, 1 = inside set valence_mode, 1
# antialias
set antialias = 1
# load the PDB files
load ... example PDB
# turn on grid mode and set it up
set grid_mode, 1
# hide everything
hide everything
# select protein
select prot, polymer
# color everything
color white
# show cartoon ribbon for protein
show cartoon
# don't show backbone for cartoons
set cartoon_side_chain_helper, on
# keep standard helix, strand, loop representations # other options: cartoon
loop, cartoon rect, # cartoon oval , cartoon tube cartoon automatic
# color cartoon white and set transparency set cartoon_color, white set
cartoon_transparency, 0.7
# select residue of interest
select roi, resi 27+31+34+37+41
# show sticks for ROIs
show sticks, roi
# hide non-polar H
hide (h. and (e. c extend 1))
# color ROIs
color atomic
color yellow, (name C* and roi)
# show H-bonds between sidechains and assign to slots dist Hbo-sc, resi 37,
resi 41, mode = 2
# hide alls labels
hide labels
# color all dashes green
set dash_color, green
# deselect all to avoid little pink squares deselect
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Hi markus,
just raytrace you figure using the ray command.
Justin
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117
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