[phenixbb] Only one solution in AutoMR with very negative LLG
Francis E Reyes
Francis.Reyes at Colorado.EDU
Wed Mar 16 08:55:09 PDT 2011
> Could someone tell me why HKL2000 couldn't find the correct C2 SP?
If you have a strong pseudotranslation (PST), you may see
alternating weak/strong reflections along the axes. HKL2000 usually
takes the most intense spots for indexing.Whether you include (or
HKL2000 picks) the weak reflections determines whether you get the
large unit cell (only the strong reflections) or the smaller unit cell
(strong and weak reflections). LABELIT will work with PST quite well
and I believe it picks up both the strong and weak reflections. It'll
output a script suitable for mosflm. However, make sure you include
images that include the strong/weak behavior (if it does exist in your
images, b/c it can be xtal orientation dependent).
Watch the integration in P2, do you notice that some (weak)
reflections (usually in between lattice lines) are missed?
> After refinement, the R went down to ~0.38, and the electron density
> fits well with my model except some flexible parts.
Congrats on solving the phase problem.
If these flexible parts are important to your biochemical question
(well as a crystallographer I would probably try to fit these parts),
you should explore other space groups.
My suggestion: solve and refine in C2. At the end of this you'll find
that  the structure is completely built, the density fabulous, but
the R/Rfree is still high or  the structure is not completely
built (there's chain breaks, other abnormalities), or  something I
haven't come across. Any of these will probably cause your structure
to get rejected or at least disputed.
Take that structure and molrep into the P2 data using AUTO for the PST
(pseudotranslation) vector (molrep will generate the second copy based
on the PST vector found in the patterson and then use that for the TF
Then take the solution and submit it to Zanuda (http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
) to find the proper origin (in case molrep found the wrong origin).
This program will test other (potential) space groups as well.
If you try this, I'd love to hear the results.
Francis E. Reyes M.Sc.
University of Colorado at Boulder
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