Hi all,
I am trying to use the formatConverter (either directly from py API or
through the gui) to convert the cns output pdb to a pdb convform file.
But somehow the atom naming is completely borked. Here an example:
CNS output:
ATOM 10 N PRO 2 -18.702 -7.034 -6.051 1.00 0.00 A
ATOM 11 CA PRO 2 -18.238 -7.114 -7.438 1.00 0.00 A
ATOM 12 HA PRO 2 -18.525 -8.049 -7.897 1.00 0.00 A
ATOM 13 CB PRO 2 -18.967 -5.959 -8.126 1.00 0.00 A
ATOM 14 HB1 PRO 2 -19.879 -6.321 -8.575 1.00 0.00 A
ATOM 15 HB2 PRO 2 -18.330 -5.531 -8.887 1.00 0.00 A
ATOM 16 CG PRO 2 -19.247 -4.983 -7.037 1.00 0.00 A
ATOM 17 HG1 PRO 2 -20.133 -4.414 -7.274 1.00 0.00 A
ATOM 18 HG2 PRO 2 -18.400 -4.323 -6.909 1.00 0.00 A
ATOM 19 CD PRO 2 -19.468 -5.800 -5.793 1.00 0.00 A
ATOM 20 HD1 PRO 2 -20.518 -6.019 -5.668 1.00 0.00 A
ATOM 21 HD2 PRO 2 -19.084 -5.281 -4.928 1.00 0.00 A
ATOM 22 C PRO 2 -16.728 -6.937 -7.554 1.00 0.00 A
ATOM 23 O PRO 2 -16.114 -7.410 -8.510 1.00 0.00 A
And this is what ccpn makes out of it:
ATOM 10 C PRO A 2 16.356 6.197 -9.520 1.00 0.00
C
ATOM 11 CA PRO A 2 17.860 6.198 -9.784 1.00 0.00
C
ATOM 12 CB PRO A 2 18.139 6.517 -11.251 1.00 0.00
C
ATOM 13 CD PRO A 2 18.730 4.221 -10.917 1.00 0.00
C
ATOM 14 CG PRO A 2 18.158 5.186 -11.921 1.00 0.00
C
ATOM 15 HA PRO A 2 18.337 6.934 -9.154 1.00 0.00
H
ATOM 16 1HB PRO A 2 17.353 7.148 -11.642 1.00 0.00
H
ATOM 17 2HB PRO A 2 19.091 7.018 -11.341 1.00 0.00
H
ATOM 18 1HD PRO A 2 18.225 3.268 -10.979 1.00 0.00
H
ATOM 19 2HD PRO A 2 19.791 4.098 -11.074 1.00 0.00
H
ATOM 20 1HG PRO A 2 17.153 4.895 -12.189 1.00 0.00
H
ATOM 21 2HG PRO A 2 18.784 5.227 -12.800 1.00 0.00
H
ATOM 22 N PRO A 2 18.464 4.872 -9.619 1.00 0.00
N
ATOM 23 O PRO A 2 15.574 6.667 -10.346 1.00 0.00
O
In particular HB1 becomes 1HB instead of HB2 as I would expect it to be.
Same for all the other proton names.
Bug or feature?
thanks justin
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117
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