Merging in radiation damaged data can indeed raise R/Rfree because the
structure factors no longer correspond to the native structure. Rather,
they are an intensity-average of the native and damaged structures, and
that can be hard to fit to a coordinate model! How much damage is too
much? I'd say its when the change in the data or "error due to damage"
becomes comparable with the lowest error you could hope to get when
fitting a model to the native data: ~20-30% (R/Rfree). This generally
happens after about 20-30 MGy (Banumathi et al. 2006; Owen et al, 2006;
Kmetko et al. 2006).
However, "redundancy" and "radiation damage" are not the same thing.
Contrary to popular belief, it IS possible to take many many exposures
from the same crystal without doing any more damage than the usual ~100
exposures. How? What manner of trickery is this? Simple! You use a
shorter exposure time.
Personally, I always think about "redundancy" or "multiplicity" in the
context of a fixed crystal "lifedose"
(http://dx.doi.org/10.1107/S0909049509004361). That is, you only get so
many seconds of shutter-open time before the crystal is dead. So, to
me, "strategy" is nothing more than deciding how to divide up those
shutter-open seconds, and the only way to increase
redundancy/multiplicity is to shorten the exposure time. Which, by the
way, is almost always a good idea.
-James Holton
MAD Scientist
On 1/24/2012 11:52 AM, Miguel Ortiz Lombardia wrote:
El 24/01/12 18:56, Greg Costakes escribió:
Whoops, I misspoke... I meant Rsym and Rmerge increase with higher
redundancies.
But then suppose that one merges data from a crystal that is degrading
while exposed, sp the data gets degraded. This is not at all unusual. In
the absence of a deep understanding of refinement, intuition suggests
that degraded data should produce degraded models. If Rwork and Rfree
are measuring anything useful they should go up redundancy in those
not-so-unusual cases. Or intuition is misguiding me again.
-- Miguel
-------------------------------------------------------------------------------
Greg Costakes
PhD Candidate
Department of Structural Biology
Purdue University
Hockmeyer Hall, Room 320
240 S. Martin Jischke Drive, West Lafayette, IN 47907
--------------------------------------------------------------------------------
** Hard work often pays of in time, but Procrastination always pays off
now **
------------------------------------------------------------------------
*From: *"Dale Tronrud"<det...@uoxray.uoregon.edu>
*To: *"Greg Costakes"<gcost...@purdue.edu>
*Cc: *CCP4BB@JISCMAIL.AC.UK
*Sent: *Tuesday, January 24, 2012 12:43:43 PM
*Subject: *Re: [ccp4bb] Problem with getting Rfree and Rf down
Is this observation about redundancies a general rule that I missed?
It seems rather surprising to me. What have results have others seen?
Dale Tronrud
On 01/24/12 07:23, Greg Costakes wrote:
snip...
Higher redundancies (>7 or so) do tend to increase overall R/Rfree.
snip...
-------------------------------------------------------------------------------
Greg Costakes
PhD Candidate
Department of Structural Biology
Purdue University
Hockmeyer Hall, Room 320
240 S. Martin Jischke Drive, West Lafayette, IN 47907
--------------------------------------------------------------------------------
** Hard work often pays of in time, but Procrastination always pays off
now **
------------------------------------------------------------------------
*From: *"Sam Arnosti"<meisam.nosr...@gmail.com>
*To: *CCP4BB@JISCMAIL.AC.UK
*Sent: *Monday, January 23, 2012 4:48:50 PM
*Subject: *[ccp4bb] Problem with getting Rfree and Rf down
Hi every one
I have some crystals in the space group P3121. I collect 180 frames of
data.
My crystals do not diffract better than at most 2.0 angstrom, but the Rf
barely goes below 23%,
and Rfree also remains somewhere between 28-33%. I have tried to refine
my data as much as I can.
I do not know whether the problem is because of the bad diffraction or
collecting extra frames.
The structure factors are also high but they get better as the crystals
diffract better.
Thanks
Sam
