[Biojava-l] Re: strange pdb
Andreas Prlic
ap3 at sanger.ac.uk
Thu Jan 12 08:41:31 EST 2006
Hi Tamas,
the Atoms have an altLoc field. - only the pdb parser did not capture
that information...
I committed a fix to cvs.
Cheers,
Andreas
On 12 Jan 2006, at 12:52, Tamas Horvath wrote:
> (wow... stupid linewrap...)It seems to me, that we need a variance tag
> for the Group or Atom object...As a beginning... The altloc is
> supposedly means variation of the atomsposition, but it seems to me,
> it makes more sense to treat the alternates asalternative groups, as
> in the cases I've so far seen, these altlocs reallyrefer to
> alternative sidechain conformations. In this case there would be aTYR
> A and TYR B conformation.
> On 1/12/06, Tamas Horvath <hotafin at gmail.com> wrote:>> Hi!> I've just
> stubled upon a strange pdb parsing fenomenon. Look at the> following
> pdb file:> ATOM 1 N GLU 326 14.783 14.947 -11.793
> 1.00 46.17> N> ATOM 2 CA GLU 326 15.471 16.220 -11.447
> 1.00 39.29> C> ATOM 3 C GLU 326 14.978 16.646 -10.075
> 1.00 37.04> C> ATOM 4 O GLU 326 13.774 16.707 -9.841
> 1.00 37.72> O> ATOM 5 CB GLU 326 15.133 17.290 -12.489
> 1.00 45.78> C> ATOM 6 CG GLU 326 16.102 18.482 -12.553
> 1.00 71.24> C> ATOM 7 CD GLU 326 15.940 19.327 -13.826
> 1.00 93.39> C> ATOM 8 OE1 GLU 326 14.901 19.198 -14.512
> 1.00101.02> O> ATOM 9 OE2 GLU 326 16.857 20.119 -14.144
> 1.00 84.50> O> ATOM 10 N TYR 327 15.913 16.885 -9.163
> 1.00 33.93> N> ATOM 11 CA TYR 327 15.604 17.298 -7.797
> 1.00 23.92> C> ATOM 12 C TYR 327 15.865 18.786 -7.632
> 1!
> .00 24.48> C> ATOM 13 O TYR 327 16.797 19.328 -8.230
> 1.00 31.71> O> ATOM 14 CB ATYR 327 16.402 16.443 -6.818
> 0.50 29.56> C> ATOM 15 CB BTYR 327 16.528 16.583 -6.799
> 0.50 30.30> C> ATOM 16 CG ATYR 327 16.280 14.990 -7.206
> 0.50 45.39> C> ATOM 17 CG BTYR 327 15.997 15.310 -6.184
> 0.50 31.62> C> ATOM 18 CD1ATYR 327 16.886 14.518 -8.371
> 0.50 44.19> C> ATOM 19 CD1BTYR 327 14.840 15.316 -5.413
> 0.50 41.31> C> ATOM 20 CD2ATYR 327 15.466 14.119 -6.496
> 0.50 38.02> C> ATOM 21 CD2BTYR 327 16.667 14.101 -6.351
> 0.50 54.42> C> ATOM 22 CE1ATYR 327 16.676 13.240 -8.828
> 0.50 27.11> C> ATOM 23 CE1BTYR 327 14.361 14.153 -4.823
> 0.50 24.22> C> ATOM 24 CE2ATYR 327 15.256 12.830 -6.944
> 0.50 27.50> C> ATOM 25 CE2BTYR 327 16.196 12.934 -5.764
> 0.50 45.82> C> ATOM 26 CZ ATYR 327 15.866 12.400 -8.1!
> 19 0.50 24.52> C> ATOM 27 CZ BTYR 327 15.041 12.970
> -5.001 0.50 38.12> C> ATOM 28 OH ATYR 327 15.666 11.127
> -8.607 0.50 51.23> O> ATOM 29 OH BTYR 327 14.567 11.824
> -4.411 0.50 40.14> O> ATOM 30 N PHE 328 15.050 19.446
> -6.825 1.00 20.97> N> ATOM 31 CA PHE 328 15.212 20.876
> -6.587 1.00 20.04> C> ATOM 32 C PHE 328 15.213 21.072
> -5.098 1.00 28.28> C> ATOM 33 O PHE 328 14.775 20.197
> -4.363 1.00 24.43> O> ATOM 34 CB PHE 328 14.061 21.656
> -7.209 1.00 22.08> C> ATOM 35 CG PHE 328 13.906 21.406
> -8.670 1.00 31.12> C> ATOM 36 CD1 PHE 328 13.164 20.320
> -9.124 1.00 23.58> C> ATOM 37 CD2 PHE 328 14.547 22.217
> -9.594 1.00 47.00> C> ATOM 38 CE1 PHE 328 13.064 20.044
> -10.465 1.00 30.40> C> ATOM 39 CE2 PHE 328 14.452 21.948
> -10.954 1.00 44.64> C> ATOM 40 CZ PHE 328 13.706
> 20.852!
> -11.386 1.00 33.12> C>> As the pdb parser goes through these it
> simply cuts off those A/B variants> of that TYR, and simply just
> parses them as similarly named atoms of the> same aa. This is really
> not a desired thing to do.> As in the pdb format description, this
> is:>> 17 Character altLoc Alternate location
> indicator.>>>> Maybe the simplest way to deal with it is to let the
> user choose, which wariant should be used...>>
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Andreas Prlic Wellcome Trust Sanger Institute
Hinxton, Cambridge CB10 1SA, UK
+44 (0) 1223 49 6891
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