VMD-L Mailing List

From: Marc Baaden (baaden_at_smplinux.de)
Date: Fri Aug 30 2002 - 04:37:22 CDT

pgrayson_at_ks.uiuc.edu said:
>> > - is it possible to color the generated surface eg via the >
>> B-factor field (.. or other options) ?
>> There's no option for it, but you could fairly easily modify the
>> script to do the coloring any way you want. Take a look at it, and if
>> you have trouble understanding what to change, we could give you some
>> advice.

OK, I have checked it, and see that right now there is a uniform color
definition via 'graphics $graphicsmol color yellow'. So where would I
be able to attribute a color to a given point/triangle ? I guess somewhere
in the procedure hull_surface, but I don't really know what to change.

>> > Is there a way to improve representation of the 'outliers' > or
>> if not eventually remove them (other than just excluding > those
>> points manually)
>> The script automatically removes triangles from the surface when they
>> are too large. Try changing the size cutoff [..]

OK, that is one kind of work-around. I guess my real problem is that for
the surface I am looking at, I need several normals depending on where I
am on the surface.

>> Did you actually generate any surfaces successfully with my script?
>> That wasn't clear.

Yes indeed I did, and they are quite how I expected them to be !
So that is very nice.
 

>>> John Stone said:
(coloring)
>> In order to do this, you would need to have a tag for each point that
>> indicates what atom it corresponds to.

Well in my particular case (the way I treat the surface), each point IS
actually an atom which has the property to be colored in its B-factor
field.

>> Alternately, if you have a
>> spatial or volumetric property that could be evaluated, it should be
>> simple to color the geometry with a transfer function that maps the
>> chosen property to colors, evaluated at each source vertex/point in the
>> surface. This is how VMD applies its coloring methods to the surfaces
>> that are produced by Surf and MSMS, they keep an atom tag with the
>> various vertices, and this tag allows VMD to go in and re-color the
>> geometry with whatever it likes, based on the atom tags it gets from
>> Surf and MSMS.

Ok, I see. That might be an option for 'additional' coloring choices.
Any 'simple' example that a tcl-ignorant like me might understand ?

>> > - part of the surface is quite curved [..]
>> Without an example image I'm not sure what the cause of the high curvature
>> is. It could simply be that you need to generate a finer mesh, or that
>> you need to manually assign per-vertex normals (average of all facets
>> that include the vertex), which would give you much better shading
>> results.

The mesh should be fine enough, but I think you are quite right about
the normals. In 85-90% of cases a similar normal direction is ok, but
for the outliers it needs to be changed (to about 90 deg of the original
one).

So far I went for the quick and dirty solution .. which is (given that my
mesh is very fine) using the actual 'atoms' in van der waals representation
which yields a kind of saucage slice surface. (I needed a figure quickly
for a talk I gave this morning .. so I had to rush). Actually it looks quite
nice.

But I will try and see if I can improve things with a proper surface using
Paul's script.

Cheers,
Marc 

-- 
 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
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