Re: [PyMOL] cartoon_transparency issue

D'uh!!!

I need to get used to always "ray" before assuming anything.

Sorry for the noise!

-----Original Message-----
From: Justin Lecher [mailto:j.l...@fz...] 
Sent: Tuesday, August 26, 2014 4:24 AM
To: pym...@li...
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
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Slashdot TV.  
> Video for Nerds.  Stuff that matters.
> http://tv.slashdot.org/
> 
> 
> 
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
> 

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