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Multicoloured Surfaces in Grasp

Cole Thomson thomson at zonker.bioc.aecom.yu.edu
Mon May 12 14:22:57 EST 1997


Steffen Graether wrote:
> 
> Using grasp, I've been trying to colour hydrophobic patches on my protein
> in a colour other than white. However, when I use the command "molecular
> surfaces"  and enter on the command line:
> 
> vc=5,rn=(1,10)

I like to do the same thing, and find it very informative.  This is
what works for me.  Color the atoms you are interested in with the
command:

c=5,rn=(1,10)
vc=a

vc=a means color the surface the same as the underlying atom.
This only works when the display for surfaces is set to "discrete
colors".
Also, remember that backbone atoms are hydrophilic.  If you want to 
avoid coloring them as hydrophobic type:

c=5,rn=(1,10),a=-ba


> 
> Residues 1-10 are white. The same thing happens if I write the command as
> a macro. Does anyone have any suggestions as to what I'm doing wrong?
> 
> Also, what do I do if I want to select two groups of residues for
> creating a surface?
> 
> rn=(1,10), rn=(30,40)

Try creating a subset that includes those two groups of atoms. Then,
when you make your surface you will have the opportunity to create
over the subset, rather than the whole molecule.  Be careful when you
do this, however, since your mouse will be connected to whatever you
defined as your subset, rather than the whole molecule.  This can 
cause you to move just that part of the molecule out of its proper
orientation with the rest of the structure. You can reconnect to the
whole molecule in the formal subset section.




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