VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 13 2005 - 10:04:22 CDT

Peter,
  The "A" and "B" aren't actually part of the residue name, they
are a separate "altLoc" field, so I don't think I want to change VMD
to treat them as part of the residue name. (It could make structure
building more troublesome since we wouldn't recognize these funny
residue names in some automated scripts for one thing)
I do see the value of identifying the "A" or "B" form of the residue,
but perhaps just having an "altloc" keyword would be just as useful,
though the atom selection would read more like this:
  resname HC4 and altloc A
  resname HC4 and altloc B

Would that be a reasonable approach, instead of changing the residue name?

  John

On Wed, Jul 13, 2005 at 10:02:52AM +0200, Peter Schellenberg wrote:
> 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 

-- 
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