# [phenixbb] Stalled refinement

Sat Apr 19 08:33:48 PDT 2014

Thank you so much Dale,
I am embarrassingly bad at doing transformation matrices. I am going to
review and repeat what you did. Your reasoning is making more sense to me.
I just wish I had a better handle on this to identify it myself. Do you
have any books/resources that might help in this regard (Not necessarily
crystallography books)?

On Sat, Apr 19, 2014 at 12:38 AM, Dale Tronrud <detBB at daletronrud.com>wrote:

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> Hi,
>
>    In P21 the equivalent positions are:
>
> xyz; -x,y+1/2,-z.
>
> In matrix form the operation to transform chain A onto the symmetry
> image of A is:
>
> Transform A -> Symmetry related A
> /-1   0   0\  /x\   / 0 \
> | 0   1   0 | |y| + |1/2|
> \ 0   0  -1/  \z/   \ 0 /
>
>    Now let's assume there are two molecules in the ASU related by
> a perfect two-fold, axis parallel to the crystal screw axis, but
> with arbitrary translations perpendicular.  The equation to transform
> chain B onto A is:
>
> Transform B -> A
>
> /-1   0   0\  /x\   /t1\
> | 0   1   0 | |y| + |0 |
> \ 0   0  -1/  \z/   \t3/
>
>
>    Now, the question is "What is the transformation that takes
> chain B directly onto the symmetry image of A?"  We can derive
> that by transforming B onto A and then transforming that by the
> crystal screw axis.
>
> Transform B -> symmetry related A
>
> /-1   0   0\  //-1   0   0\  /x\   /t1\\   / 0 \
> | 0   1   0 | || 0   1   0 | |y| + |0 || + |1/2|
> \ 0   0  -1/  \\ 0   0  -1/  \z/   \t3//   \ 0 /
>
> Now simplify:
>
> / 1   0   0\  /x\   /-t1\   / 0 \
> | 0   1   0 | |y| + | 0 | + |1/2|
> \ 0   0   1/  \z/   \-t3/   \ 0 /
>
> / 1   0   0\  /x\   /-t1\
> | 0   1   0 | |y| + |1/2|
> \ 0   0   1/  \z/   \-t3/
>
>    What we get is an identity operator with a translation.
>
> Note, I didn't make any other assumptions.  Whenever you have space
> group P21 and two-fold ncs with the same symmetry axis direction you
> will get pseudo-translation.
>
>    With your crystal the ncs matrix is not aligned with the y
> axis all that well.  I haven't calculated it exactly but it seems
> to be about 10 deg away.  That must be enough to wipe out the
> Patterson peak and the pseudo-translation check in xtriage.
>
>    As a side note, you mentioned that you didn't think this was
> pseudo-translation because the translation was not 0.5.  A translation
> of 0.5 could lead to pseudo-centering which is a special case of
> space group C2 and half your reflections would be systematically
> weak and this can cause problems with the free R.
>
> Dale Tronrud
>
>
>
> On 4/18/2014 2:16 PM, Yarrow Madrona wrote:
> > Hi Dale,
> >
> > You know a lot more (and probably have forgotten more)
> > crystallography theory than I will every know. But I thought that
> > rotational and translational NCS can be completely separate from
> > the space group symmetry. They can become confused when the NCS
> > operator is close to a crystallographic symmetry axis. I have P21
> > symmetry between dimers but there is only one dimer in the unit
> > cell. They appear to have near perfect 2-fold symmetry between them
> > on the b-axis (according to the transformation matrix). However,
> > the translation between them is not close to 1/2 of a unit cell as
> > would be expected for a 2(1) screw axis. This makes sense because I
> > don't see a peak on the patterson map but I do see a peak on the
> > self rotation. X-triage also confirms the first part.
> >
> > I also get a translation of (0, 0.3, 0.3) but I thought this
> > wouldn't show up as translational "NCS" because it was not near
> > 0.5. I thought the difference between the vectors would not
> > perfectly superimpose to give a strong peak on a patterson map.
> >
> > Please correct me if I am wrong (because I probably am). It is
> > entirely possible I sound like an idiot. If so please let me know.
> > crystallography. If you have a good reference please let me know.
> >
> > -Yarrow
> >
> >
> > On Fri, Apr 18, 2014 at 9:34 AM, Dale Tronrud
> > <detBB at daletronrud.com <mailto:detBB at daletronrud.com>> wrote:
> >
> > Hi,
> >
> > I don't see how you can not have translational ncs.  You are in
> > space group P21 and have an ncs two-fold parallel to y. Doesn't
> > this combination have to give rise to translational ncs?
> >
> > I may have screwed up my paper matrix multiplications but I come
> > up with a translational ncs of about (0, 0.3, 0.3) in fractional
> > coordinates.  If the translation were 0.3333 you would only see
> > strong reflections for k+l=3n.  This would result in a lot of weak
> > data and higher than expected free R's.
> >
> > Of course, xtriage should be screaming bloody murder and you
> > should be seeing the peak in the Patterson.  I'm confused.
> >
> > Dale Tronrud
> >
> > On 4/17/2014 6:05 PM, Yarrow Madrona wrote:
> >> There is no significant peaks for translational NCS. I also
> >> didn't see anything in the patterson map.
> >
> >> However, the Multivariate Z score L-test gives 6.218. Also the
> >> observed Centric reflections are more intense than they should
> >> be but I don't suspect twinning in a monoclinic space group.
> >
> >> -Yarrow
> >
> >
> >> On Thu, Apr 17, 2014 at 4:37 PM, Paul Adams <pdadams at lbl.gov
> >
> >
> >> What does triage say about translation NCS?
> >
> >
> >> On Thu, Apr 17, 2014 at 4:25 PM, Yarrow Madrona
> >
> >> Hello,
> >
> >> I using the latest stable build of phenx.refine (1.8.4) I
> >> recently collected data, processed and obtained an MR solution
> >> using phaser. I am stuck trying to refine with an Rfree sitting
> >> at 40%
> >
> >> I really want to know if the high Rfree is due to poor data
> >> quality or if non-crystallographic symmetry involving a near
> >> perfect two fold rotation between the two molecules in the ASU
> >> could somehow impede refinement. Stats and other information is
> >
> >> -Yarrow
> >
> >
> >> Visually, the quality of the data is marginal at best
> >> (streaky/ice rings in many frames) despite good processing stats
> >> from XDS. Processing with mosflm or HKL2000 managed to index but
> >> failed pretty bad in integration and scaling.
> >
> >> Phaser gave high TFZ scores for 2 molecules in the asu (see
> >> below).
> >
> >> Density for a cholesterol like ligand shows up even though not
> >> present in the search model.
> >
> >> MolRep Self rotation shows rotational symmetry.
> >
> >
> https://www.dropbox.com/s/2zsajl5o091k50r/CYP142A2-032814_21_rf%20copy.pdf
> >
> >
> >> The 2 molecules in the ASU are related by almost a 2 fold
> >> rotation:
> >
> >> Rotation matrix for chain A to chain B:
> >
> >> new_ncs_group rota_matrix    1.0000    0.0000    0.0000
> >> rota_matrix 0.0000    1.0000    0.0000 rota_matrix    0.0000
> >> 0.0000 1.0000 tran_orth     0.0000    0.0000    0.0000
> >
> >> center_orth   15.2016    0.5245   33.7070
> >
> >> rota_matrix   -0.9860   -0.1636   -0.0309 rota_matrix   -0.1659
> >> 0.9511    0.2605 rota_matrix   -0.0132    0.2620   -0.9650
> >> tran_orth      34.3310  -24.0033  107.0457
> >
> >> center_orth   15.7607    7.2426   77.7512
> >
> >> RMSD, B onto A = 0.0007 after phaser RMSD, B onto A = 0.347
> >> after one round of refinement in phenix
> >
> >
> >> Refinement using aniostropically corrected data (ucla web
> >> server: Services.mbi.ucla.edu/anisoscale
> > <http://Services.mbi.ucla.edu/anisoscale>
> >> <http://Services.mbi.ucla.edu/anisoscale>) did not improve the
> >> Rfree in refinement.
> >
> >
> >> Statistics are listed below:
> >
> >> UNIT CELL: 51.487 88.923 89.592 90 97.15 90 P21
> >
> >> RESOLUTION     NUMBER OF REFLECTIONS    COMPLETENESS R-FACTOR
> >> R-FACTOR COMPARED I/SIGMA   R-meas  CC(1/2)  Anomal  SigAno
> >> Nano LIMIT     OBSERVED  UNIQUE  POSSIBLE     OF DATA   observed
> >> expected                                      Corr
> >
> >> 5.99        8280    1927      2087       92.3%       3.1% 3.3%
> >> 8246   35.09      3.5%    99.8*    20*   0.909    1296 4.30 14606
> >> 3401      3487       97.5%       3.3% 3.5%    14580 33.37
> >> 3.8%    99.9*    11*   0.843    2273 3.53       17961 4244
> >> 4445       95.5%       3.8% 3.9%    17944   31.11 4.4%    99.8*
> >> -2    0.789    2721 3.06       21954    5068 5221       97.1%
> >> 4.9% 5.1%    21933   24.81      5.6% 99.7*    -2    0.780    3455
> >> 2.74       25741    5830      5933 98.3%       7.6% 7.6%    25713
> >> 18.88      8.6%    99.5*    -2 0.782    4165 2.51       27859
> >> 6311      6483       97.3% 10.8% 10.8%    27824   14.06     12.3%
> >> 99.1*    -2    0.774 4385 2.32       31336    6979      7084
> >> 98.5%      14.9% 15.3%    31296   10.49     16.8%    98.5*    -4
> >> 0.748    5095 2.17       32396    7347      7567       97.1%
> >> 22.3% 22.7% 32341    7.46     25.4%    97.3*    -7    0.728
> >> 5055 2.05 32254    7339      8047       91.2%      33.1% 33.5%
> >> 32075 5.06     37.5%    94.8*    -6    0.724    5155 total
> >> 212387 48446     50354       96.2%       7.8% 7.9%   211952
> >> 16.57 8.8%    99.7*    -3    0.768   33600
> >
> >> Processing with mosflm or HKL2000 managed to index but failed
> >> pretty bad in integration and scaling.
> >
> >
> >> Phaser:
> >
> >> SOLU SET RFZ=27.5 TFZ=24.2 PAK=0 LLG=1711 RF++ TFZ=64.6 PAK=0
> >> LLG=3610 LLG=4865
> >
> >
> >> _______________________________________________ phenixbb mailing
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> >> <mailto:phenixbb at phenix-online.org>
> >> <mailto:phenixbb at phenix-online.org
> > <mailto:phenixbb at phenix-online.org>>
> >> http://phenix-online.org/mailman/listinfo/phenixbb
> >
> >
> >
> >
> >> -- Paul Adams Deputy Division Director, Physical Biosciences
> >> Division, Lawrence Berkeley Lab Division Deputy for Biosciences,
> >> Department of Bioengineering, U.C. Berkeley Vice President for
> >> Technology, the Joint BioEnergy Institute Laboratory Research
> >> Manager, ENIGMA Science Focus Area
> >
> >> Building 64, Room 248 Tel: 1-510-486-4225 <tel:1-510-486-4225>,
> > Fax: 1-510-486-5909 <tel:1-510-486-5909>
> >> http://cci.lbl.gov/paul
> >
> >> Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121
> >> Berkeley, CA 94720, USA.
> >
> >> Executive Assistant: Louise Benvenue [ LBenvenue at lbl.gov
> > <mailto:LBenvenue at lbl.gov>
> >> <mailto:LBenvenue at lbl.gov <mailto:LBenvenue at lbl.gov>> ][
> > 1-510-495-2506 <tel:%5B%201-510-495-2506> ]
> >
> >
> >
> >
> >> _______________________________________________ phenixbb mailing
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> >> http://phenix-online.org/mailman/listinfo/phenixbb
> >
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> >
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