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I'll jump in here, and avoid the question entirely. Since running MR on an isomorphous crystal gives the same answer as just stuffing in the model and running some rigid body refinement, however you decide to handle your R free flags, you should do the same thing in both cases. The model is the same. Dale Tronrud On 11/21/11 14:47, Michael Thompson wrote: > ----- Forwarded Message ----- > From: "Michael Thompson" <[log in to unmask]> > To: "e dodson" <[log in to unmask]> > Sent: Monday, November 21, 2011 11:30:17 AM GMT -08:00 US/Canada Pacific > Subject: Re: [ccp4bb] LESS MR pleae.. 1.95A, different phase > > A question regarding the plea for less MR (which I support): > > There have been several recent instances in which I have used the solution of an isomorphous structure to do rigid body refinement for a new crystal (as described by Eleanor). It has always produced good results. My question is about how to best handle the free set of reflections when doing this? I have heard a number of differing opinions about whether or not it is important to carry the freeR flags from the original structure over to the new data set. I have heard equally convincing arguments from both sides, so my young and impressionable mind does not know who to believe. I was hoping I could get an opinion from the "advocates for less MR." > > Sorry for hijacking this thread, but hopefully it will provide some insight that is relevant to the original post. > > Thanks! > > Mike > > > > > ----- Original Message ----- > From: "Eleanor Dodson" <[log in to unmask]> > To: [log in to unmask] > Sent: Monday, November 21, 2011 2:23:21 AM GMT -08:00 US/Canada Pacific > Subject: Re: [ccp4bb] LESS MR pleae.. 1.95A, different phase > > Just a plea for less molecular replacement. > > If you get a new crystal of a known protein with the same cell > dimension as youur old crystal, the most likely scenario is that it has > the same group, and you really should not try MR - use the previous > solution as input to do rigid body refinement, and then > a) the R factor will tell you if this is a reasonable hypothesis (it > usually is..) and > b) you dont have this awful problem of not being able to compare the > solutions.. > > Eleanor > > On 11/20/2011 03:57 PM, Napoleão Valadares wrote: >> 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: [log in to unmask] <mailto:[log in to unmask]> >>> 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 >>> >> >> >