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One comment I'd like to add here is that in the presence of pseudo-translational ncs that is nearly colinear with crystal axes you will have a significantly higher R-value. This may be a serious problem with some reviewers when your R~30% on a 2A dataset. It is completely justified then to have the R-values calculated excluding absences. Perhaps refinement programs should do this automatically if the pseudo-translation is detectable? (perhaps as advisory output) On Sat, 2012-03-17 at 06:37 +0000, Eleanor Dodson wrote: > pseudo translation is very common and usually does not pose a serious > problem. you have to be careful about assigning the space group, since a > translation od x,y,z=1/2 will generate absences for l = 2n+1 which may > suggest a screw axis along c . But since your space group is P21 that isn't > a problem here. > > Your next problem is how to rebuild the structure! > > Eleanor > > > > > On Mar 16 2012, xiaoyazi2008 wrote: > > >Thanks all! > > > > In addition to the pseudo translation problem, the model I used for MR is > > really a partial model with low quality. It could make it more > > complicated. I guess the MR solution is right since phaser gave very high > > Z-score (up to 60, maybe it is not real, too high to be true). It is > > possible that P1 is the hope. > > > > Are there any cases that structures were determined only by experimental > > phasing with pseudo translation? > > > >Nice weekend! > >zhihong > > > > > > > > > >On Mar 15, 2012, at 1:54 AM, [log in to unmask] wrote: > > > >> Dear Zhihong, > >> > >> Refinement stuck at 55% Rfree (which is essentially random), means that > >> you do not have found the correct MR solution. For me the prime suspect > >> is the space group. In my experience pseudo translation or any almost > >> crystallographic NCS will easily confuse automatic space group > >> determination programs like pointless and it is often trickey to find > >> out which symmetry is crystallographic and which is > >> non-crystallographic. > >> > >> Since P21 is fairly low symmetry, I would reprocess your data in P1 and > >> just naively run all your favorite molecular replacement programs > >> (phaser, molrep, epmr, phenix, etc.) in P1. I would try them all since > >> there are subtle difference between these programs and one may succeed > >> where the others fail. Once you have a solution which refines (Free > >> Rfactor drops below say 40% in P1) you can try to figure out what the > >> true, higher symmetry space group may be. Your true space group may even > >> be P1, with pseudo P21 symmetry! > >> > >> Good luck! > >> Herman > >> > >> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of > >> xiaoyazi2008 Sent: Thursday, March 15, 2012 6:12 AM To: > >> [log in to unmask] Subject: Re: [ccp4bb] Help! weird thing > >> > >> Dear all, Thank you very much for all the great suggestions on my case. > >> Yes, I run the latest version of Phaser in Phenix. The analysis showed > >> that there is one non-origin distinct peak more than 15 angstroms from > >> the origin. 44.1% origin: FRAC 0.000 0.042 0.500 (ORTH -15.7 2.8 103.5) > >> I managed to find four copies with the latest Phaser. After 50 cycles of > >> rigid body refinement and 50 cycles of jelly body refinement, Rfree/R > >> goes around 55/52. It is really hard for me to do model building at this > >> point, because there is pretty much no new density. > >> > >> Compare to model building and refinement with normal dataset (no pseudo > >> translation NCS), are there any special tricks or tips for structure > >> determination from dataset with pseudo translation? > >> > >> Thanks again! > >> > >> Have a nice evening or morning or afternoon! > >> Zhihong > >> > >> On Mar 12, 2012, at 10:16 AM, Randy Read wrote: > >> > >>> Airlie points out that what I said about the ccp4i interface wasn't > >>> correct! In order to keep the ccp4i interface in synch with the version > >>> of Phaser, we've started distributing the ccp4i files with the source > >>> code. The ones on our website are for an older version of Phaser, but > >>> the latest ones will come with the Phenix download that gives you the > >>> latest executable. > >>> > >>> Apologies to anyone who was quick enough to download and install the > >>> wrong ccp4i files already! > >>> > >>> Best wishes, > >>> > >>> Randy Read > >>> > >>> On 12 Mar 2012, at 16:47, Randy Read wrote: > >>> > >>>> Yes, the current version of Phaser will do the same test that xtriage > >>>> carries out, and if it finds a sufficiently high non-origin Patterson > >>>> peak, it will automatically characterise the translational NCS and use > >>>> this for molecular replacement. This is working pretty well in our > >>>> tests. > >>>> > >>>> In the near future you will be able to get the current version of > >>>> Phaser as part of the upcoming CCP4 release, but at the moment the > >>>> easiest way to get it is to download a recent version of Phenix. You > >>>> should be able to run that through ccp4i by downloading and installing > >>>> the updated GUI files from our website (and getting ccp4i to interpret > >>>> the command "phaser" as "phenix.phaser"). > >>>> > >>>> Best wishes, > >>>> > >>>> Randy Read > >>>> > >>>> On 12 Mar 2012, at 16:06, Anastassis Perrakis wrote: > >>>> > >>>>> Hi - > >>>>> > >>>>> I agree with Garib that its likely a pseudo-translation issue. I > >>>>> also agree with that the advice he gives is correct, but ... ... > >>>>> since I am evidently less smart to follow all these steps, I like to > >>>>> use phenix.xtriage that will tell me if there is pseudo-translation > >>>>> or not, and will give a p-value for that being significant. Its at > >>>>> the end of the text output. > >>>>> > >>>>> I am not sure if Phaser deals these days with pseudo-translation - I > >>>>> guess Randy can tell us. If not, there is a very simple trick to make > >>>>> Phaser work with pseudo-translation, but since I threw the ball to > >>>>> Randy's court and he told me the trick a few years ago, I will let > >>>>> him explain only if needed ;-) > >>>>> > >>>>> Best, > >>>>> > >>>>> Tassos > >>>>> > >>>>> On Mar 11, 2012, at 12:55, Garib N Murshudov wrote: > >>>>> > >>>>>> Hi > >>>>>> > >>>>>> Could you please check: 1) If there is psedotranslation. It could > >>>>>> be done by using sfcheck, molrep, ctruncate or calculating patterson > >>>>>> map and displaying using coot at 8-10 sigma level (it is my > >>>>>> favourite method for analysis of pseudo translations), whole unit > >>>>>> cell ( a bit bigger than whole unit cell). Then if you see large no > >>>>>> origin peak (very likely along one of the axis, could be a). If yes > >>>>>> then you have several options: using phaser - 1) reduce cell, find > >>>>>> solution in smaller cell and then expand; 2) use molrep to solve. > >>>>>> When there are two copies related with pseudo translation molrep can > >>>>>> give you solution; 3) as far as I am aware latest version of phaser > >>>>>> works with pseudo translation. If you have pseudtranslation you > >>>>>> should be aware that even if you solve the structure starting R > >>>>>> factors could be 70-80%. Then you may want to do 40 cycles of rigid > >>>>>> body and 40-100 cycles of ljelly body 2) Check your space group in > >>>>>> pdb and mtz file. They may not be consistent. > >>>>>> > >>>>>> I hope it helps. > >>>>>> > >>>>>> Garib > >>>>>> > >>>>>> On 11 Mar 2012, at 07:33, xiaoyazi2008 wrote: > >>>>>> > >>>>>>> Hi All, > >>>>>>> > >>>>>>> I have an interesting thing to share. 2.3A dataset with good > >>>>>>> quality, P21 Partial model is available (~60% of the target > >>>>>>> protein). It seems that there are 4 copies in the ASU > >>>>>>> (Matthews_coef 2.6, 53%solvent) Molecular replacement gave two > >>>>>>> copies of the model (Z scores are R6.2, T6.2, R6.8, T13.4). The > >>>>>>> solution is very clear. It could not locate the rest two copies. > >>>>>>> > >>>>>>> However, a quick refmac5 refinement gave a very high R factor. The > >>>>>>> funny part is the symmetry operation in Coot. As shown in the JPEG > >>>>>>> figure, it looks like there should be another two copies (based on > >>>>>>> strong fo-fc green map), which locate in the empty space between > >>>>>>> models found by Phaser. > >>>>>>> > >>>>>>> Why is that Phaser could not find the remaining two copies even > >>>>>>> there are strong fo-fc density? Any suggestions... > >>>>>>> > >>>>>>> > >>>>>>> Thanks a lot! > >>>>>>> > >>>>>>> Zhihong > >>>>>>> <weird thing.jpg> > >>>>>> > >>>>>> Garib N Murshudov > >>>>>> Structural Studies Division > >>>>>> MRC Laboratory of Molecular Biology > >>>>>> Hills Road > >>>>>> Cambridge > >>>>>> CB2 0QH UK > >>>>>> Email: [log in to unmask] > >>>>>> Web http://www.mrc-lmb.cam.ac.uk > >>>>>> > >>>>>> > >>>>>> > >>>>> > >>>>> P please don't print this e-mail unless you really need to > >>>>> Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member > >>>>> Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. > >>>>> B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 > >>>>> 20 512 1954 Mobile / SMS: +31 6 28 597791 > >>>>> > >>>>> > >>>>> > >>>>> > >>>> > >>>> ------ Randy J. Read Department of Haematology, University of > >>>> Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 > >>>> 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road > >>>> E-mail: [log in to unmask] Cambridge CB2 0XY, U.K. > >>>> www-structmed.cimr.cam.ac.uk > >>>> > >>> > >>> ------ Randy J. Read Department of Haematology, University of > >>> Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 > >>> 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road > >>> E-mail: [log in to unmask] Cambridge CB2 0XY, U.K. > >>> www-structmed.cimr.cam.ac.uk > >>> > >> > > > > >