Dear Alastair, I really like the feature of shelxl which writes the cif-file (required for deposition to the CCSD) including all restraints, constraints, the data, and the coordinates. The program shredcif extracts the ins-file and the hkl-file, which are checksum protected against manual editing. With this and the backward compatibility of shelxl it is actually not impossible to reconstruct what was available at deposition time. For the RNA polymerase I, both data and ins-file only cover 4.5MB of data, i.e. not too much to handle by a data base.
I don't mean to promote shelxl here, but rather the method of providing a (checksum protected) means to repeat the last refinement cycle totally independent from outer resources. Cheers, Tim On 04/04/2014 06:36 PM, Alastair Fyfe wrote: > [...] > bypassing the impossible task of recording/reconstructing the program > version and options used. > > On 04/04/2014 09:13 AM, Gerard Bricogne wrote: >> I replied in too great a rush - it is the Rfree, or the Rfree-Rwork gap, >> that would go up a lot if a structure originally refined at low >> resolution >> with targeting to an external high-resolution one was re-refined without >> that targeting. >> >> Gerard. >> >> -- >> On Fri, Apr 04, 2014 at 04:55:03PM +0100, Gerard Bricogne wrote: >>> Dear Nat and Tim, >>> >>> On Fri, Apr 04, 2014 at 08:18:06AM -0700, Nat Echols wrote: >>>> On Fri, Apr 4, 2014 at 1:57 AM, Tim Gruene <t...@shelx.uni-ac.gwdg.de> >>>> wrote: >>>> >>>>> A more up-to-date reason is that programs calculate R values very >>>>> differently. If you take a PDB file refined with program X and put it >>>>> into program Y you easily get discrepancies greater than 5%. >>>>> >>>> This is actually pretty rare - usually it's only 1-2% at most. >>>> Discrepancies like 16.5% versus 30.9% usually indicate that there's >>>> something wrong or misleading in the annotation of the entry, and often >>>> mean that you can't even reproduce the R-factor with the specified >>>> program. >>>> >>>> -Nat >>> It could also be that such a structure is the result of a >>> refinement >>> against low-ish resolution data that was restrained by "targeting" it to >>> another similar structure that was refined against higher-resolution >>> data, >>> so as to retain the good local geometry of the latter in spite of the >>> shortage of data at low resolution. This is perfectly legitimate, and >>> was >>> first done by Oliver Smart in BUSTER under the acronym of "LSSR", >>> outlined >>> in an ACA 2008 Abstract then fully described in Acta Cryst. D68, 368-380 >>> (2012). A similar feature has also become available in REFMAC and >>> PHENIX. >>> >>> The problem is that the deposition process is very likely to >>> have lost >>> track of the recourse to that method, so that the outcome of the >>> refinement >>> cannot be reproduced from the deposited data in an automated environment >>> such as the EDS server. >>> >>> This may not be the case with the structure Tim was mentioning, >>> but it >>> provides an opportunity to point out that the use of some recent >>> approaches >>> to improving refinement at low resolution may need further attention >>> at the >>> deposition stage to ensure reproducibility of the results from the >>> deposited >>> information. >>> >>> >>> With best wishes, >>> Gerard. > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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