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, [email protected] 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:[email protected]] On Behalf Of
xiaoyazi2008 Sent: Thursday, March 15, 2012 6:12 AM To:
[email protected] 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: [email protected]
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: [email protected] 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: [email protected] 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
