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
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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 BiologieStructurale 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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