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
> >>> 
> >> 
> >
> >
>