*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk ***
This points to another issue that would be interesting to have discussed in the ccp4bb: the guys at EBI always renumber the solvent molecules, ions and/or ligands following a so-called uniformatory convention during coordinate deposition. This is rather annoying because it leads to interested readers of the paper associated to a structure not being able to follow the discussion while looking at the coordinates without getting heavily confused. What is the experience of other people ? Do the guys in Rutgers also do this ? Would it be possible to make a lobby and get the PDB NOT TO CHANGE anything we don´t want to have changed in the structures that are supposed to be submitted and dsposited BY US? This is as if I went to the bank to deposit some money in what's theore- tically my account and that it was actually the clerk that told me how much I have to deposit ! Alternatively, would it be possible to incorporate a small program into the ccp4i gui to apply exactle the changes the PDB do and keep this fuzzy numbering during the end stages of refinement and then for the writing up of the paper ? Maybe some feedback with the PDB-desk would be appreaciated in this case. Best, Xavier On Wed, 06 Dec 2006 8:14:45 +0000 Garib Murshudov wrote: *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** There is a resolution in the output. In fact two lines: REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.36 Refmac does not write REMARK 2. Refmac writes only REMARK 3 Garib On 6 Dec 2006, at 07:45, R.P. Joosten wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk ***> > > Dear All, > > The REMARK 2 (resolution) card is also missing from the Refmac > output. There are quite a few programs that rely on that value. Can > that one be added as well? > Adding the matrix weight to the header may help us to reproduce the > results of the original refinement. At the moment, this is still > very difficult to say the least. > > Cheers, > Robbie Joosten > Centre for Molecular and Biomolecular Informatics > > Bernhard Rupp wrote: >> *** For details on how to be removed from this list visit the *** >> *** CCP4 home page http://www.ccp4.ac.uk ***>> Dear All, >> refmac writes a very useful header on top >> of the PDB files which it refined. That header is >> again read by autodep at the EBI and becomes >> part of the PDB file. >> I think there is one important parameter missing >> which is needed to reproduce the refinement: >> The matrix weight used. Could that be included in >> the refinement REMARK section? >> Thx, br >> -------------------------------------------- >> Bernhard Rupp >> www.ruppweb.org >> -------------------------------------------- >
