[ccp4bb]: re hetgroup geometry and SF deposition

[Kim Henrick <henrick@ebi.ac.uk>]

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ccp4bb@dl.ac.uk
 
For deposition of structure factors to the PDB - the requirement
is highly recommended but still at this stage there is no mandatory
requirement. A document of SF is given in
   http://autodep.ebi.ac.uk/sf.html

re the comments on un-scaled un-merged data and anomalous data items
There are plans to request in addition to the SF list used in
refinement to get these data as described in
   http://autodep.ebi.ac.uk/un_merged_hkl.html


re dictionaries
the service http://www.ebi.ac.uk/msd-srv/chempdb/
 allows for download of idealised coordinates as
 PDB or mmcif (chem_comp categories NOT atom_site categories) or XML
 these are from Corina - we as yet still have not finalised our
 internal expanded VEGA atom types to all CNS/CCP4-REFMAC energy types
 so that we can export CNS and refmac5 dictionaries - this is
 still in progress and is taking a lot more trouble than expected.

Please note that this does not allow for new structures like in 
- the PRODRG server
  http://davapc1.bioch.dundee.ac.uk/prodrg  (also does SHELX topologies)

Also please note the Corina idealised coordinates for metal complexes
have problems and are not to be fully trusted. In this case perhaps the
PDB best coordinates are better either from here or 
- the HICup site by Gerard Kleywegt
  http://xray.bmc.uu.se/hicup/welcome.html

CORINA can give idealised coordinates as well (not dictionaries)
http://www2.chemie.uni-erlangen.de/software/corina/index.html

Idealised coordinates to dictionaries is a ccp4 program

VEGA atom descriptors are described in
 http://users.unimi.it/~ddl/vega/index.htm


As far as the errors in chemistry for molecules bound in the PDB entries
for all new submissions the EBI and RCSB and PDBj make all efforts
to detect problems and comment back to the authors - we do not
reject bad chemistry and in almost all cases the authors do
respond with a correction.

For the legacy PDB entries - apart from tagging poor geometry
in the relational database there is little that can be done.

We do check now (for at least the last 12 months) all chirality and
geometry automatically for hetgroups but we also had to rely on
the original's to get the starting chirality to get smiles to get
idealised coordinates - so for example we picked the wrong COA for a
chirality error in C10 that was detected when we had a deposition
with the correct COA C10 chirality - at least the C10 has what
the text book says is correct that does not exclude that COA in the entry
we originally picked as the 'best' for resolution/Rfactor is not 
correct - it may be an alternative isomer - so it will be renamed as
a new molecule. Your email discussion has allowed us and a submittor
to realise that there is another COA with an error in a sugar carbon
and this will be corrected. None of these types of error are in my
experience with dealing with submissions over the last few years the result
of any deliberate action but the results of people simply making 
mistakes in trying to do the best job possible in interpretation
of the exp results.


This discussion has shown a wide spread agreement that standards and
structure factors should be applied and deposited. We can just
hope that we can make SF's mandatory.

kim henrick