[PyMOL] cartoon_transparency issue

[Markus H. <mh...@cd...>]

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


-- 
Markus Heller, Ph.D.
NMR Scientist
CDRD - The Centre for Drug Research and Development
2405 Wesbrook Mall, Fourth Floor | Vancouver, BC  V6T 1Z3 | Main: (604) 827-1147
Direct: (604) 827-1122 | F: (604) 827-1299 | E: mh...@cd... | www.cdrd.ca






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