Dear Laurent, 1) Refmac mentions gaps explicitly in the LINK records, the PDB does it in a REMARK record (by comparing the atom records to the sequence of your crystallised construct). If you just remove the gap-LINKs before deposition (without adding TER records) it should work.
2) First of all you have to make sure you deposit your raw reflection file (i.e. NOT the output from Refmac). Also anytime you run Refmac, you should start from the same reflection file. If this is not the source of the problem then you can look at other things. What happens after the 0-th refinement cycle when you rerun your model through Refmac? Do R and R-free go down to your previous values? This sometimes happens and has something to do either with the solvent treatment or with scaling. As long as you deposit the total B-factors after TLS (in the form of ANISOU records) and have a proper description of any special refinement settings (twinning, non-default solvent mask parameters) in the header of the PDB file you deposit, you can ignore the problem. HTH, Robbie http://www.cmbi.ru.nl/pdb_redo http://xtal.nki.nl/PDB_REDO > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Laurent Maveyraud > Sent: Wednesday, February 05, 2014 08:11 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] depositing PDB files from refmac > > 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 > > > > > -- > ---------------------------------------------------------- > 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 > ----------------------------------------------------------
