[phenixbb] Stalled refinement
Yarrow Madrona
amadrona at uci.edu
Sat Apr 19 08:24:24 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
> pseudo-translation. If you had that your crystal would be nearly
> 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.
> > Otherwise I will never learn more about the fundamentals of
> > 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
> > <mailto:pdadams at lbl.gov>
> >> <mailto:pdadams at lbl.gov <mailto:pdadams at lbl.gov>>> wrote:
> >
> >
> >> What does triage say about translation NCS?
> >
> >
> >> On Thu, Apr 17, 2014 at 4:25 PM, Yarrow Madrona
> >> <amadrona at uci.edu
> > <mailto:amadrona at uci.edu>
> >> <mailto:amadrona at uci.edu <mailto:amadrona at uci.edu>>> wrote:
> >
> >> 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
> >> below. Thank you for any help you can give.
> >
> >> -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,
> >> Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor,
> >> 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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> >
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