Wim Vranken wrote:
> Hi Gary,
>
> Did you use the formatConverter?
er yup
> If you use the Pdb format, then the input has to be an official PDB
> file.
The input was a series of pdbs from xplor joined with aquas joinpdb
tool... is this a pdb or pseudo pdb?
> Otherwise use pseudoPdb, and select the naming system. It should
> handle multiple models without problem (though there might be
> problems if it does not recognize the end-of-model string).
ok
here is an example
REMARK xplor energies: bond: 1.401440 angle: 93.713848 impr: 8.271418
vdw: 889.776738 rama: -18863.684832
REMARK
REMARK Done with original Marvin pass3 protocol
REMARK
MODEL 1
ATOM 1 N MET 1 41.915 12.072 38.490 1.00 1.00 XXXX
ATOM 2 HT1 MET 1 42.382 11.331 37.930 1.00 1.00 XXXX
ATOM 3 HT2 MET 1 41.242 12.590 37.889 1.00 1.00 XXXX
ATOM 4 HT3 MET 1 41.406 11.634 39.283 1.00 1.00 XXXX
....
ATOM 2431 HD21 ASN 149 73.328 5.241 28.631 1.00 1.00 XXXX
ATOM 2432 HD22 ASN 149 74.996 5.518 28.478 1.00 1.00 XXXX
ATOM 2433 C ASN 149 71.493 2.229 26.917 1.00 1.00 XXXX
ATOM 2434 OT1 ASN 149 71.674 2.432 25.728 1.00 1.00 XXXX
ATOM 2435 OT2 ASN 149 70.893 1.264 27.361 1.00 1.00 XXXX
ENDMDL
MODEL 2
ATOM 1 N MET 1 -6.216 -17.216 -1.975 1.00 1.00 XXXX
ATOM 2 HT1 MET 1 -7.250 -17.313 -1.950 1.00 1.00 XXXX
ATOM 3 HT2 MET 1 -5.908 -16.573 -1.217 1.00 1.00 XXXX
ATOM 4 HT3 MET 1 -5.779 -18.149 -1.838 1.00 1.00 XXXX
ATOM 5 CA MET 1 -5.800 -16.662 -3.295 1.00 1.00 XXXX
.....
ATOM 2431 HD21 ASN 149 -6.656 -32.925 -22.475 1.00 1.00 XXXX
ATOM 2432 HD22 ASN 149 -7.835 -31.784 -22.041 1.00 1.00 XXXX
ATOM 2433 C ASN 149 -4.645 -34.743 -18.222 1.00 1.00 XXXX
ATOM 2434 OT1 ASN 149 -4.380 -35.600 -19.049 1.00 1.00 XXXX
ATOM 2435 OT2 ASN 149 -4.267 -34.772 -17.063 1.00 1.00 XXXX
ENDMDL
END
>
> Wim
>
> .
>
regards
gary
--
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Dr Gary Thompson
Astbury Centre for Structural Molecular Biology,
University of Leeds, Astbury Building,
Leeds, LS2 9JT, West-Yorkshire, UK Tel. +44-113-3433024
email: [log in to unmask] Fax +44-113-2331407
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