Hi Randy, thank you for your help. Today we collected at the CLS two newer crystals of this form. I will process them and see, if they give me better results. For the dataset that I have done mor. rep, here is information from the headers of solutions P6222: LLG 2194 in p32: LLG 6840 C222: LLG=5252 C2: LLG 7942 P62: LLG 4058 Z-scores are very high, too, between 40 and 60. Refinement of any of these solutions gives Rfree around 50-55%, actually, it goes up at every cycle of refinement. Randy, what is the best file to send to you: which space group for the sca or mtz file , which solution? Maia Randy J. Read wrote:

Hi Maia,

If it's a molecular replacement issue, we might be able to help. I'd be happy to look at your data.

All the best,

Randy

On Aug 25 2009, Maia Cherney wrote:

...

Thank you Peter for your reply.

I will try the p1 expansion. Thank you for the suggestion. And really data look very good, the Rmerge is very low, chi squares are around one, looked like a perfect data set to me;

one molecule in AU (in p6222). The model is exactly the same protein solved in two other space groups.

And it's not one crystal, all these bipyramids are like this. I can send you my p1.sca if you are curious to look at it.

Maia

Peter Zwart wrote:

...

Hi Maia,

Two points:

1) :

Given that fact that you can process the data in p622, you can expand the data to p1:

phenix.reflection_file_converter mydata.sca --sca=p1.sca --expand_to_p1

Eventhough this is not the same as having 'real' p1 data, you know that the data merges well in p622, so no harm is done (or at least not a lot).

Do you have pseudo translational symmetry by any chance? I wasn't able to find any relation between the two provided unit cells. It is very curious that their volume are equal though.

2):

The fact that you cannot solve it might also be due to the fact that your MR model is incorrect for some obscure reason.

HTH

Peter

2009/8/25 Maia Cherney :

...

Hi everybody,

I have two types of hexagonal crystals: rods and bipyramids with dimensions 150x150x83 (rods) and 142x142x93 (bipyramids). Both types of crystals give the same spacegroup P6222. However, the rods gave a good solution and refined to low R factors, whereas the bipyramids give a solution with high LLG and Z-score, but don't refine at all (R factors around 50%). The xtriage does not indicate any twinning. Lower symmetry spacegroups (trigonal and monoclinic) have the same problem: give solutions with high scores that would not refine. The resolution is 2.3A. Unfortunately, the dataset processed in p1 has only 60% completeness (as it was collected according to p3 strategy). Should I try to solve in p1 with this low completeness? What can be a problem?

Maia

Peter Zwart wrote:

...

Good point.

For now the best thing to do is to read the RvsR paper cited in the text. I'll add a section to the manual as well.

Ideally of course, xtriage should make its own judgement. Some code is there, but I took it out as it is not well-tested (and didn't do the job)

P

2009/8/25 Pavel Afonine :

...

Hi Peter,

do you have any guidance to how interpret this table summarized somewhere in the documentation? Otherwise it looks a bit cryptic to me (I tried it while ago, may be it is improved now). Alternatively, it would be nice if Xtriage prints out its own verdict based on that table.

Thanks! Pavel.

On 8/25/09 10:47 AM, Peter Zwart wrote:

> Subsequently, run > > phenix.xtriage p1data.mtz reference.structure.file=MR.1.pdb > > and start interpreting the RvsR tables. > > > > _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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