Dear Randy,
Thanks very much for your detailed explanation and helpful advice. I have
run the phaser job just as you have said. This is the result.
The resolution of this dataset is 2.45A.
=====================================================================
I added the three commands to phaser job for all alternative space group of
P212121:
TNCS USE ON
TNCS NMOL 4
TNCS PATT PERCENT 80.0
The phaser got a SINGLE solution for space group P22121, and Rval=88.2
SOLU SET RFZ=14.5 TFZ=22.3 PAK=0 +TNCS PAK=0 +TNCS PAK=0 +TNCS PAK=0
LLG=2565LLG=4322
SOLU SPAC P 2 21 21
SOLU 6DIM ENSE ensemble1 EULER 91.7 89.4 90.3 FRAC 0.49 0.51 0.99 BFAC
0.00
SOLU 6DIM ENSE ensemble1 EULER 269.3 89.4 90.2 FRAC -0.01 -0.00 0.74
BFAC 0.00
SOLU 6DIM ENSE ensemble1 EULER 269.0 89.1 90.0 FRAC 0.49 -0.00 1.00 BFAC
0.00
SOLU 6DIM ENSE ensemble1 EULER 91.5 89.3 90.2 FRAC 0.99 0.51 0.74 BFAC
0.00
After 50 cycles rigidbody refinement, R/Rfree=0.36/0.37
After 50 cycles restraint refinement (with jellybody refine and twin
refine), R/Rfree=0.31/0.35
After several cycles of coot model building and restraint refinement,
R/Rfree=0.27/0.31
After finding waters, R/Rfree=0.2478/0.2984
===================================================================
If I run phaser job without those three added commands, the phaser got
single solution at P21212 space group (Rval=0.3%):
SOLU SET RFZ=17.0 TFZ=20.1 PAK=0 LLG=457 TFZ==16.2 RFZ=16.3 TFZ=62.1
PAK=0
LLG=2599 TFZ==19.8 (& TFZ=59.0 PAK=0 LLG=2403) LLG+=(2608 & 4349)
LLG=4200
TFZ==22.2 PAK=0 RFZ=10.8 TFZ=56.4 PAK=0 LLG=5751 TFZ==22.5 LLG=9274
TFZ==27.5
SOLU SPAC P 21 21 2
SOLU 6DIM ENSE ensemble1 EULER 90.0 90.7 270.1 FRAC -0.00 0.26 0.13 BFAC
-4.09
SOLU 6DIM ENSE ensemble1 EULER 271.2 89.4 90.3 FRAC 0.01 0.24 -0.38 BFAC
-3.00
SOLU 6DIM ENSE ensemble1 EULER 270.3 90.8 270.1 FRAC 0.50 -0.25 -0.12
BFAC -1.25
SOLU 6DIM ENSE ensemble1 EULER 87.5 90.6 270.4 FRAC 0.02 0.26 -0.37 BFAC
11.58
And the electron density is worse than the P22121 solution.
======================================================================
Just as I have said last email, I can also get single solution at P212121
space group,
and after 50 cycles rigidbody refinement and 50 cycles restraint refinement
with jellybody and twin, I can get R/Rfree=0.30/0.33.
But the electron density is worse than the P22121 solution, so I do not
carry out the model building in coot.
=======================================================================
My questiones:
1) Is the P22121 solution is my correct solution? These three solutions
really confused me.
2) Why the R/Rfree is high even after I have good electron density and have
found waters? (R/Rfree=0.478/0.2984 for 2.45A data)
3) What's the function of the command "TNCS USE ON"? Is it necessary?
4) I found if I used twin refinement in refmac5, the R/Rfree would decrease
about 0.02 comparing to without twinn refinement. Is it reasonable? Is
there any tNCS refinement options in refmac?
Thanks for your help.
Best wishes,
Qixu Cai
2012/7/31 Randy Read <rj...@cam.ac.uk>
> Hi,
>
> The second Patterson peak is twice the first (considering lattice
> translations, where 1 is equivalent to 0 modulo 1), and then if you triple
> the first vector you'll get minus the first vector (again considering
> lattice translations, i.e. 3/4 is equal to 1 - 1/4 which is equivalent to
> -1/4), which is equivalent by symmetry to the first vector so wouldn't
> appear in the peak list. So the Patterson indicates 4 copies separated by
> 0, 1, 2 and 3 times the top Patterson vector, in approximately the same
> orientation.
>
> We've haven't fully dealt with the complications of multiple tNCS-related
> copies in Phaser yet, but for this type of case there is a reasonable
> treatment. You should add two commands to the Phaser job:
>
> TNCS NMOL 4
> TNCS PATT PERCENT 80
>
> The first says that the Patterson translation is repeated 4 times, and the
> second will cause the second Patterson peak to be ignored.
>
> I'd suggest repeating the Phaser run with these commands and making sure
> that you end up with the same solution as you got when the tNCS was
> ignored. When tNCS is ignored, it's possible to end up with a solution
> that is only partially correct, which would be one explanation for having
> some molecules that look better in density than others.
>
> Best wishes,
>
> Randy Read
>
> On 31 Jul 2012, at 13:11, Qixu Cai wrote:
>
> > It's a P212121 dataset. I have used phaser to find four solution in ASU.
> >
> > This is the phaser log file:
> > ------------------------------------------------------------
> > PEUDO-TRANSLATIONAL NCS VECTOR
> > --------------------------------------------------------------
> >
> > Space Group : P 21 21 21
> > Patterson Symmetry: P m m m
> > Resolution of All Data (Number): 2.45 49.00 (22968)
> > Resolution of Patterson (Number): 5.00 9.99 (2364)
> > There were 2 non-origin distinct peaks (i.e. more than 15 angstroms
> from the
> > origin)
> >
> > <!--SUMMARY_BEGIN-->
> > 84.1% origin: FRAC 0.500 0.000 0.250 (ORTH 32.0 0.0 32.2)
> > 72.2% origin: FRAC 0.000 0.000 0.500 (ORTH 0.0 0.0 64.4)
> > <!--SUMMARY_END-->
> >
> > More than one pseudo-translational ncs vector found
> > Correction factors will not be applied
> >
> >
> > PS: I have used phenix.xtrige and found the p-value of
> > pseudo-translational ncs is very little, which indicates the exist of
> > the pseudo-translational ncs. And no twin found in this dataset.
> >
> > Now the problem is two in the four molecules of an ASU have worse
> > electron density than the other two molecules. And after rigidbody and
> > restraint refinement by refmac without "twin refinement", the R/Rfree
> > is a little high (0.33/0.36). And if I turn on the "twin refinement"
> > in refmac, the R/Rfree is 0.30/0.33.
> >
> > So, my question is, there is not twin in my data but
> > pseudo-translational ncs, is it suitable to use "twin refinement" in
> > refmac, which has a good R/Rfree result.
> >
> > Thanks a lot for your help.
> >
> > Best wishes,
> >
> > Qixu Cai
> >
> >
> > 2012/7/31, Eleanor Dodson <eleanor.dod...@york.ac.uk>:
> >> More details - what do you mean by pesudo-translational symmetry ?
> >> Are there two molecules related by a translation vector? or its it
> >> something more complicated?
> >> Eleanor
> >>
> >> On 31 July 2012 10:47, Qixu Cai <caiq...@gmail.com> wrote:
> >>
> >>> Dear all,
> >>>
> >>> Can I use the "twin refinement" to refine the pesudo-translational
> >>> symmetry dataset?
> >>>
> >>> Thanks a lot for your help.
> >>>
> >>> Best wishes,
> >>>
> >>> Qixu Cai
> >>>
> >>
> >
> >
> > --
> > Qixu Cai
> > Email: caiq...@gmail.com
> > School of Life Sciences,
> > Xiamen University, Fujian, China
>
> ------
> 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: rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
>
>
