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
>>>
>>
>
>
--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266
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