(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 <[EMAIL PROTECTED]> 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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