On Friday, October 28, 2011 08:29:46 am Boaz Shaanan wrote:
> Besides, I thought that by now there are some standards on how data should
> be processed
> (this has been discussed on this BB once every few months, if I'm not
> mistaken).
If this is true, I must not have got the memo!
I hear differences of opinion among senior crystallographers, even just
considering discussions at our local research meetings, let alone in the
context of world-wide practice.
- Where to set a resolution cutoff?
- Use or not use a criterion on Rmerge (or Rpim or maximum scale factor or
completeness in shell)?
- Use all images in a run, or limit them to some maximal amount of decay?
- Empirical absorption correction during scaling?
- XDS? HKL? mosflm?
> Isn't that part of the validation process that so many good people have
> established?
> Also, to the best of my knowledge (and experience) referees (at least of
> some journals)
> are instructed to look into those issues these days and comment about them,
> aren't they?
>
> Cheers,
> Boaz
As to what reviewers have access to, at best one sees a "Table 1" with
summary statistics. But rarely if ever do we see the protocol or
decisions that went into the processing that yielded those statistics.
And more to the point of the current issue, a reviewer without access
to the original diffraction images cannot possibly comment on
- Were there unexplained spots that might have indicated a supercell
or other strangeness with the lattice?
- Evidence of non-merohedral twinning in the diffraction pattern?
- Was the integration box size chosen appropriately?
- Did the diffraction data clearly extend beyond the resolution limit
chosen by the authors?
I hasten to add that I am not advocating for a requirement that the
diffraction images be sent to reviewers of a manuscript!
But these are all examples of points where current opinion differs,
and standard practice in the future may differ even more.
If the images are saved, then the quality of the data extracted from
them may improve using those not-yet-developed programs and protocols.
So there is, to me, clearly some value in saving them.
How to balance of that value against the cost? - that's another question.
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
