Reconstructing the refinement may be necessary in some cases but there
are other applications (pdb-wide map statistics, development of map
analysis tools, quick model vs map checks) where access to the
depositor's final map would be sufficient. Perhaps the coefficients are
in fact included in many of the available mmCIF files? I should check..
thanks,
Alastair
On 04/04/2014 09:52 AM, Nat Echols wrote:
On Fri, Apr 4, 2014 at 9:36 AM, Alastair Fyfe <[email protected]> wrote:
The topic brings up a question that I've been wondering about for some
time, perhaps someone can enlighten me. Why is it not standard practice to
deposit map coefficients along with structure factors ? Unlike image
deposition there are no significant storage or file format issues. This
would preserve a record of the "final" refinement used for publication,
bypassing the impossible task of recording/reconstructing the program
version and options used.
There *are* file format issues, they're just very silly. I think the
problem is that the PDB deposition service ignores most columns in MTZ
files, even with standard labels that have not changed for years. If you
deposit the reflections as mmCIF instead, and use the designated mmCIF
dictionary items for your map coefficients (or Fcalc, phases, etc.), it
will preserve them. For instance:
http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=structfact&structureId=4OW3
I still don't think this solves the problem of faithfully recording the
refinement protocol - how do you know what method was used to calculate the
maps?
-Nat
