Miguel wrote:
my priority list:Q: Do you mean 'alone' as if the other atoms were not in the file?
Yes
If so, then that is not compatible with RasMol/Chime behavior.
but of much more use
yes, I want to be able to visualize binding pockets (where solventQ: Is that what you want?
and/or a ligand is in contact with the protein under experimental
conditions)
OK
Q: Is this high-priority or low-priority for you?
-. MessageCallBack output at least compatible to RasMol
echo
show selected group *
set picking
correct PDB atom number
-. access to the color scheme
set helix color red (now color structure should use red for helix parts)
set carbon color green (from now on color cpk should use green for carbons)
-. rockets with
http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=1ne6
Exception in thread "AWT-EventQueue-2" java.lang.NullPointerException
at javax.vecmath.Tuple3f.set(Tuple3f.java:161)
-. surface rendering
-. script access to distances, angles, torsions ... surface area ...*--> MessageCallBack
center [0.0, 0.0, 0.0] output *-->
-. color hbonds type
-. general use of atom expression, e.g.
bond 23:A.CA 23:A.O1
-. further operators for advanced scripting bound and count *-->
-. --noscript
(size should be viewer size)
-. molecule
-. script accessing PDB file
-. stereo
Regards, Jan
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