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: ga...@mrc-lmb.cam.ac.uk
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
