From: Napoleão Valadares
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
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From: Tim Gruene
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
----------
From: Tim Gruene
Dear Napo,
to illustrate Felix Frolow's comment, take Solution-1 and the new data
to refmac5 and run 'rigid body refinement'. I would not be surprised if
you get a reasonable map with nearly the same R/Rfree as your MR
solution, which means that this solution and the one from MR are
equivalent (because of the freedom of choice for the origin some space
groups allow you).
Tim
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
From: Felix Frolow
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
On Nov 20, 2011, at 07:42 , Napoleão Valadares wrote:
----------
From: Napoleão Valadares
Date: 20 November 2011 15:57
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
----------
From: Barnali Chaudhuri
"one origin to rule them all" works in the
reciprocal space ....
----------
From: Jim Pflugrath
A source of confusion is that we are using two
different definitions of "origin". In the a graphics program
sense (coot, pymol), the origin is always at xyz coordinate (0, 0, 0). I
think that's what Napo means by "present the same cell and origin."
However, imagine a crystal upon which we put a unit
cell box with one corner labelled (0, 0, 0) and the opposite corner labelled
(1, 1, 1) in fractional coordinates. We can use the unit cell box as a
"ruler" to read out positions in the crystal. Within the
crystal are our molecules in a repeating lattice. Now suppose we move our
unit cell box around the crystal while keeping the molecules fixed in the
lattice. Do you see how the relative coordinates of the molecules with
respect to that unit cell box will change even though the crystal does not
change nor do the molecules in the crystal?
I know this doesn't explain everything about
"origins" as not every point in most crystal lattices can be an
origin, but I will save that concept for another day. I just wanted to
note the apparently different definitions of origin in this thread.
Jim
Sent:
Sunday, November 20, 2011 9:57 AM
From: Napoleão Valadares
The problem was resolved with your help, and in fact there was no problem, except that I was unaware of the alternative origins. I promise I'm reading more about it. :$
A side note: I collected another crystal, different crystallization condition but same cell parameters, and followed Eleanor Dodson suggestion, just did a rigid body and the map looks just like the others.
Thanks you for all the answers, I'm learning a lot by trying to follow (and understand) your different suggestions, and by following this list in general. It is a good reading.
Best regards,
Napo
A side note: I collected another crystal, different crystallization condition but same cell parameters, and followed Eleanor Dodson suggestion, just did a rigid body and the map looks just like the others.
Thanks you for all the answers, I'm learning a lot by trying to follow (and understand) your different suggestions, and by following this list in general. It is a good reading.
Best regards,
Napo
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