Currently the documentation says to use "ignore {water}" implying that without this, water will be included in the surface.
I want to make an isosurface for water. I had great difficulty doing this. I suggest that either the default be changed NOT to ignore water, or else there needs to be a way to tell the isosurface command to INCLUDE water (I could not find any such method).
I ended up having to change, in the PDB file, the group names from HOH to ZYX (WAT did not fool it), and also the oxygens to nitrogens in both the element column and the final column of the PDB file. That allowed me to get a surface with "isosurface solvent".
2. I want to color the surface by MEP. It appeared that I had no problems setting the partial charges with
{hydrogen}.partialCharge = 0.41
#{oxygen}.partialCharge = -0.82
{nitrogen}.partialCharge = -0.82
The documentation says that
isosurface resolution 6 solvent map mep
will use the partialCharge atom properties. It did not (surface was all blue). Is this a bug or a problem in the documentation?
3. The MEP section of the isosurface documentation says that "if MEP is followed by PROPERTY xxxx" it will be used instead of partial charges. However,
isosurface resolution 6 solvent map MEP property partialcharge
produced an all-blue surface. Is this a bug?
4. In order to color the surface, I omitted "MEP":
isosurface resolution 6 solvent map property partialcharge
This produced the default yellow-green-blue surface. But I want a red-white-blue surface as is conventional for MEP. OK, so this worked
isosurface resolution 6 solvent map MEP property partialcharge colorscheme "rwb"
except that the "red" was pink and the "blue" was deep blue, despite the isosurface report claiming "isosurface full data range -0.82 to 0.41 with color scheme spanning -0.82 to 0.41".
I tried a few things to get a redder color at the reddest end of the colorscheme, without success.
Is there some way I can get the "red" in the "rwb" color scheme to be redder (more saturated)?
Thanks! -Eric
------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
