Hi Dan,
We do check for those, although is a pre-calculation since we take the
original PDB file and translate the ASU into an standard frame of reference,
the CIAU in the VIPERdb convention (this puts all of the capsids exactly in
the same orientation). Then we calculate all the interfaces, finding the
residues
involved in inter-subunit contacts. I must say, though, that the clashes we
have
found exist in structures coming from homology modeling only, not Xray (so
far ;)
The transformed coordinates are then served and used in VIPERdb.
Out of interest, do you check the results for 'clashes' between
> interface atoms? The presence of many clashes would indicate that
> something had gone wrong in the process. If I understand correctly
> this could happen if the ASU were incorrectly specified.
>
--
0 | Mauricio Carrillo Tripp, PhD
/ | Department of Molecular Biology, TPC6
0 | The Scripps Research Institute
\ | 10550 North Torrey Pines Road
0 | La Jolla, California 92037
/ | [EMAIL PROTECTED]
0 | http://viperdb.scripps.edu/
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