VMD-L Mailing List

From: Peter Schellenberg (peter.schellenberg_at_ipht-jena.de)
Date: Wed Jul 13 2005 - 03:02:52 CDT

Hi

Many thanks for the thorough responses. As already mentioned,
one time consuming and not very elegent method is to just select
the atom indexes, which for the chromophore AHC4 and BHC4 in
1s1y.pdb looks somewhat odd, for example:

mol selection { (index 678 682 684 1222 1224 1226 1228 1230
1232 1234 1236 1238 1240 1242 1244) and not water}

mol selection { (index 677 681 683 685 1223 1225 1227 1229 1231
1233 1235 1237 1239 1241 1243) and not water}

and do not forget about all the other aminoacids ....

What about the possibility for a syntax like:
mol selection (resname AHC4)
mol selection (resname BHC4)

or even better
 mol selection (resname A*)
 mol selection (resname B*)

Rasmol and Pymol can somehow distinguish between AHC4 and
BHC4 and do not draw bonds between AHC4 and BHC4, however
easy selection of one of the two conformations is again not possible.

regards Peter

Dr. Peter Schellenberg
Institute for Physical High Technology Jena
Dept. of Biotechnical Microsystems
Albert -Einstein -Str. 9
D-07745 Jena