"one origin to rule them all" works in the reciprocal space ....
________________________________________
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Napoleão
Valadares [n...@if.sc.usp.br]
Sent: Sunday, November 20, 2011 10:57 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 1.95A, different phases, maps look the same, R/Rfree
22/24, wrong space group? - No alternative origin
Thank you all for the replies. Felix Frolow, Dan Leahy, Hans Brandstetter, Boaz
Shaanan and Tim Gruene you really helped a lot.
I think I understand it now, I always thought the "one ring to rule them all"
translated in the crystallography realms to "one origin to rule them all". That
probably means I have a long road in front of me.
I'm still half confused, I definitely need to read more, as much as I read
about symmetry and space groups I never seem to improve or get a better
understanding, but I'll keep trying.
About the same origin:
The pdbs of both Solution-1 and Solution-2 present the same space group and
cell, as observed opening the pdbs as text files or in pymol. When I open both
maps on coot they are not superposed but present the same cell and origin.
If I open both solutions on pymol they clash. If I generate the symmetry mates
of both solutions none of them are superposed, instead they clash. But I think
they are related as you all pointed, I'll check it out.
Thank you all for your kind answers and your patience with a beginner.
Regards from a sunny Brazil,
Napo
On 11/20/2011 2:58 AM, Felix Frolow wrote:
Napoleao,
It is so called alternative origins play a game with you. You do not change
your structure by shifting 1/2 translation (or even combination of these
translations)
into directions of the main axes of your unit cell. Structure factors after
this operation stay the same, however phases change systematically, producing
however the same
map features.
Would I be a begin crystallographer now, I would read a bit more old fashioned
books
on crystallography such as probably Jensen and Stout…
FF
Dr Felix Frolow
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail: mbfro...@post.tau.ac.il<mailto:mbfro...@post.tau.ac.il>
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Nov 20, 2011, at 07:42 , Napoleão Valadares wrote:
Hello,
I'm observing a very strange phenomena (at least to me, I'm a beginner). It is
related to symmetry (I think).
I got a data set at 1.95A (I/Sigma 3.5, R-Factor and R-meas < 35% in the last
shell) and a partially refined solution with R/Rfree 22/24, 166 aminoacids
observed and around 30 solvent molecules. I'll call this Solution-1. The
refinement was smooth, the densities were very clearly "asking" for the correct
missing side chains and the map looks good.
The space group I'm using is P212121, pointless and XDS agree with that (but me
and pointless both have a long history of being wrong about space groups).
Phenix.xtriage says there's no twinning.
I took Solution-1 and used it as a template in a molecular replacement in the
same space group (P212121) using the same mtz as the one used to refine the
template. I got a different (not superposed in space) solution (called
Solution-2, scores by Phaser RFZ=24.2 TFZ=33.0 PAK=0 LLG=1413 LLG=1899) that
was readily refined in Phenix to R/Rfree 24/26 without any solvent molecule.
- The solutions are not superposed in space, although they are near-identical
and can be superposed yielding a C-alpha rmd =0.001.
- Both structures present VERY similar density maps. The maps are not
superposed in space, but when you "run the chain" in one map in Coot and do the
same in the other it they the present exactly the same features. It is
impossible to ignore their similarities.
- Both structures and maps present the same origin and unit cell.
- If I add to Solution-2 the equivalent solvent molecules of Solution-1 (I did
this by superposing Solution-1 to Solution-2 then copy/pasting the solvent
molecules), the R/Rfree become 22/24. This is a clear indication that the
solutions are related.
- I can't find any MR solutions using the same template and space groups P222,
P2221 and P21212.
How two different sets of phases can yield maps with the same features? What is
happening, wrong space group? I have a feeling my lack of experience is the
problem.
Thank you.
Regards,
Napo
