From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 05 2005 - 15:43:27 CDT

Hi guys,
  I finally had a chance to write code to support selections based on
the PDB alternate location identifiers. At present, atoms with no
altloc identifier will get an altloc code of "" and atoms with an
altloc identifier will get the "A", "B", etc, as specified in the
PDB file. Once loaded into VMD, you can then do things like make
atom selections with the keywords:
  altloc "" or altloc "A"

You can then trivially select which parts of the structure to display
by switching "A" to "B", etc. I think this will help immensely when
people are viewing PDB structures with this information.
I haven't added logic to the automatic bond determination routines
to prevent bonding between atoms with different altloc identifiers,
but I'll add that to my TODO list.

If you guys are interested in trying out a test version, let me know.

  John

On Thu, Jul 14, 2005 at 08:38:46AM +0200, Eduard Schreiner wrote:
> John Stone wrote:
> >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
> >
> >
> Hey John,
>
> this approach is much better than changing the residue name: pdb entries
> are treated properly, it would be as easy to use as other selections.
> Sounds very good.
>
> Eddi
>
> --
>
> --
>
> =======================================================================
> Eduard Schreiner e-mail: eduard.schreiner_at_rub.de
> Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-22121
> Ruhr-Universitaet Bochum - NC 03/52 Fax: ++49 (0)234/32-14045
> D-44780 Bochum http://www.theochem.rub.de
> =======================================================================

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