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re [ccp4bb]: generate pdb header
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re data_harvesting for CCP4
The latest version of CCP4 will o/p mmcif files
for several of the programs mosflm/scala/truncate/mlphare/restrain/refmac
at the end of a refinement one can make a xx.tar.gz file of these files
and submit these for deposition
At this stage the atom coordinates are not o/p in mmcif format
and would have to be submitted as a separate file (within a set of files).
(see at end of this note about deposition to the ebi)
It is not possible to convert an existing CCP4 logfile into
harvest format. Harvest files are only generated by using
the latest version of CCP4.
The semi-automatic tracking of data through CCP4 will be become
easier when the next version of mosflm is released - this will
impose a responsibilty of the user to start labelling data sets
and the labels will be included into the first mtz file. Subsequent
use of these mtz files will transfer labels to both 'harvest results
files for each step' and to subsequent mtz file headers. It is however
the users responsibilty to track each stage of a structure solution
and carry out ultimate book keeping. The harvest files from each stage
can then be accumulated into a compressed tar file and submitted for
simplified deposition. In addition - it hasnt yet been used in the
real world and we dont know how it will mesh with different in-house
practical use of different software. As it is common to say start with
denzo, use CCP4 then cns then o then refmac - only experience will
allow resolution of any practical difficulties.
The work done at ESRF/BNL and other sync sites to add data labels
to image headers will further smooth the flow of information from
data collection to refinement by having mosflm and hkl2000 read
the headers and transfer this to derived files. This is not yet
[for NMR structures the EBI is at the momment initiating a comprehensive
harvest solution with the cooperation with the new CCPN and in particular
with a workshop to held at the EBI on the 7-8Feb 2000]
One can also use CNS and use the mmcif_deposition macro
which was in
this only does refinement
there is also in pdb format (read by autodep)
The CNS macros (and the equivalent XPLOR PDB macros) deal only
with information known for refinement.
Both CCP4 pdbset and the CNS/XPLOR PDB macros can generate PDB SEQRES
records for sequence, although there are problems in some cases with
different conformations and the enthusiam that the macros add all,
including water to SEQRES.
There is also info to be written out from hkl2000 (denzo/scalepack)
although this isnt currently the same as CCP4 (mosflm/scala)
As far as deposition - the ebi is still using PDB(BNL) legacy code in
the form of autodep (autodep.ebi.ac.uk) as we in the final stages of
developing a completely new submission system that can handle these
files. We have not as yet modified autodep to read mmcif files - a
function this software could never do.
However, until the new system is ready, if you want to use CCP4 or cns
mmcif o/p in your deposition, then please do the following:
1. Start an autodep submission, upload the files and email
email@example.com to say you have done this.
2. We will convert the files to autodep and allow you to continue the