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
Re: [ccp4bb] 1.95A, different phases, maps look the same, R/Rfree 22/24, wrong space group? - No alternative origin
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 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Napoleão Valadares [n...@if.sc.usp.br] Sent: Sunday, November 20, 2011 9:57 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 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.
Re: [ccp4bb] 1.95A, different phases, maps look the same, R/Rfree 22/24, wrong space group? - No alternative origin
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 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
