Good morning CCP4 list
I am trying to deposit structures refined with refmac (latest version
5.8.0049, windows seven), and I have two issues raised at the validation
step :
1) there are chain breaks in my protein (for disordered loops). Refmac
adds a LINKR record for the description of the break. These are rejected
at the validatin step : they are not recognized as valid.
If I remove them (and add the TER record at the end of each chain that
refmac keeps removing), I have a warning since residues 154 and 160 are
not properly linked....
I didn't find anything for the appropriate description of chain breaks
in the descriptin of the PDB format.
2) the R/Rfactor computed by the validation server (either sfcheck or
refmac) are quite high : my refinement run gives me 0.188/0.220 when the
PDB gives 0.24/0.264 (sfcheck) or 0.20/0.23 (refmac). And, indeed, if I
feed to refmac the refined structure it has just produced, I get more or
less the same R/Rfree than the PDB.
I do use TLS refinement (1 TLS group per chain, 6 chains with NCS), and
input them as fixed TLS parameters. TLS contributin is added to Bfactors
and ANISOU lines).
How could I handle this properly ? Or should I just ignore this ?
thaks !
laurent
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Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr
P I C T --- Plateforme Intégrée de Criblage de Toulouse
Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089
Département Biologie Structurale et Biophysique
http://cribligand.ipbs.fr http://www.ipbs.fr
205 route de Narbonne 31077 TOULOUSE Cedex FRANCE
Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994
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