Re: [Jmol-users] color molecular surface by the color of underlying atoms

[Daniel C. <dan...@gm...>]

Hi,
I am trying to color the molecular surface for specific residues of
interest. Based on 2 related posts (Nov 10 and Nov 29 ) I have tried a few
things that do not quite meet my needs. Perhaps one of these approaches can
be altered to produce the desired result.

Method 1
set usercolorscheme red yellow purple green orange
isosurface select(*:V) ignore { ( *:X or *:W or *:Y or hoh ) }  molecular
map property groupid
I don't fully understand the map property command - As far as i can tell, it
colors different residue types by different colors. e.g. all tyrosines
orange, all lysines purple etc.  However, I would like to specify particular
colors for every residue number independent of the residue type. e.g. Ser2
red, ser3 purple etc.

Method 2:
define amino2 2:V
isosurface surf2 select (amino2)  sasurface opaque red
define amino3 3:V
isosurface surf2 select (amino3)  sasurface opaque purple
etc.
This method allows me to assign the desired colors at each residue number.
However, unlike method 1 (which has a smooth continuous surface) , there are
jagged gaps between each residue surface and the image lacks the aesthetics
that are required for publication/presentation.

Method 3:
{2:V}.property_color = 1
{3:V}.property_color = 2
set usercolorscheme red purple
isosurface sasurface map property_color colorScheme "user"

As reported by others, this gives an error on my version of Jmol (11_8_21):
script ERROR: invalid argument
----
         isosurface saSurface map >> property_color << colorscheme "user"

I'd appreciate any suggestions,

Daniel