[phenixbb] unusual maps and Rfree for 1.75 structure

Nathaniel Echols nechols at lbl.gov
Sat Apr 16 20:21:48 PDT 2011

On Sat, Apr 16, 2011 at 7:50 PM, Yuri <yuri.pompeu at ufl.edu> wrote:
> So I am inclined to reprocess my data in P 4 2 2. Are these "symptoms" of a
> possible wrong space group assignment? Is there something else obvious I am
> overlooking?

I don't know enough to comment on the systematic absences, but if
Xtriage doesn't indicate any problems with the resolution cutoff,
severe anisotropy, twinning, etc., my suggestion would be to look at
the images to make sure you indexed them correctly.  The command
'labelit.index' is your friend here - it will look for evidence of
pseudotranslation in the diffraction patterns, which the integration
software tends to overlook.  Ignoring the weak spots in the images
will usually still result in good scaling statistics and easy MR
solutions, and probably won't trigger any warnings in Xtriage, but it
will result in abnormally high R-factors.  (I'm not sure how common
this type of error is, but I once wasted several months trying to
refine against incorrectly processed data, so it's always the first
thing I suggest looking at.)

(By the way, if you're using the Xtriage GUI, the summary tab may be a
little misleading - interpreting the raw numbers is very subjective,
and I tried not to make the feedback too alarmist.  So the absence of
obvious warnings may not mean that everything is okay.  If you send
the Xtriage log file to help at phenix-online.org we may be able to make
a more definitive judgement.)


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