"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.
"Moreover I found that the colors, although clearly showing the
expected pattern for the data plotted, it was also having strange
behavior: it was giving a color to
certain regions that was not representative of the values."
Could you please elaborate? This is distressing. I do know that
there is averaging between 4 boxes to create a value at the common
vertex, but are you suggesting something even more problematic? I
have never looked into the quantitative behaviour of the VMD volume
slice option since it appears qualitatively correct to me.
It is not really easy to explain with words. Showing would have been
easier.
Anyways I plot a property of a bilayer system: this property is high
in the tail region, low in the
head groups region, and medium in the solvent.
With the volumeslice it looks like. averything is fine except in the
head group region which is
shown low on the slice but in the "middle" of the head region is get
the same color than the
tail region (representative of high values).
Note that I do not give volume map to VMD but I build it with it from
raw data. That might be the
problem. I've not been looking further. The only thing sure is that I
have no control of the
colors on the slice in this way. I may need to create an new
representation after changing the
color scale.
XAvier.
Chris.
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