VMD-L Mailing List

From: Eduard Schreiner (eduard.schreiner_at_theochem.ruhr-uni-bochum.de)
Date: Thu Jul 14 2005 - 01:38:46 CDT

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 

-- 
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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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