[gmx-users] g_spatial and vmd volume slice

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Feb 18 18:38:46 CET 2009

Dear XAvier,

>> "I have played with this recently and could not find the way to set  
>>  or  change the colors on the volume
>> slice."
>> see my previous post about how to do this with black/white and  
>> gimp/ photoshop
> I did not find any mention of this in your previous post. But it is ok.

Sorry for not being clear. I didn't have a web address to give you at  
that time since it had not appeared on the web yet.  Here it is:

quoting http://www.gromacs.org/pipermail/gmx-users/2009-February/039765.html

a) representation volumeslice
b) graphics--> represenations --> change coloring method to "volume"
c) graphics-->colors-> color scales --> change to white/black
d) graphics-->colors-> color scales --> slide the offset and midpoint
until you see the level of detail that you want
e) render this and take it to gimp or photoshop, change the background
to transparent, false color the density that remains, and overlay it on
a white background or perhaps overlay it on an exactly scaled picture of
one representative conformation (you can do this exactly by loading in
the correct structure along with the .cuge file to vmd and changing the
representation to output two separate files at exactly the same


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