[phenixbb] Stalled refinement
Kay Diederichs
kay.diederichs at uni-konstanz.de
Fri Apr 18 15:53:11 PDT 2014
Hi Yarrow,
of course the data quality will suffer but ultimately it depends on the
amount of splitting - as long as the integration profile covers both
parts then the total intensity is conserved, and recovered.
I have seen many datasets with split reflections that were usable for MR
and refinement. But I doubt that many of these would be suitable for
experimental phasing.
best,
Kay
Am 18.04.14 23:21, schrieb Yarrow Madrona:
> Hi Kay,
>
> Looking at the data I can see that many of the spots are actually split.
> I guess this may be causing problems in refinement if split spots are
> integrated as a single spot?
>
>
> On Fri, Apr 18, 2014 at 2:17 PM, Kay Diederichs
> <kay.diederichs at uni-konstanz.de <mailto:kay.diederichs at uni-konstanz.de>>
> wrote:
>
> It is a good idea to try several data processing programs in
> difficult cases.
>
> BTW the latest MOSFLM can also integrate two (or more) lattices.
>
> Pls report your results.
>
> Kay
>
>
> Am 18.04.14 22:59, schrieb Yarrow Madrona:
>
> Thanks Kay,
>
> XDS kicked out a lot of reflections. There were about 23,000
> rejected
> reflections out of ~ 190,000 collected. I can clearly see
> another minor
> lattice in many frames and I presume that the rejections are
> coming from
> the minor lattice that was not selected. I was thinking of
> processing
> with EVAL15 to see if I get better results. Thanks for your
> help. Maybe
> respond off-line as this is a discussion maybe more suited for
> another
> mailing list (CCP4?).
>
> -Yarrow
>
>
> On Fri, Apr 18, 2014 at 7:11 AM, Kay Diederichs
> <kay.diederichs at uni-konstanz.__de
> <mailto:kay.diederichs at uni-konstanz.de>
> <mailto:kay.diederichs at uni-__konstanz.de
> <mailto:kay.diederichs at uni-konstanz.de>>>
>
> wrote:
>
> Hi Yarrow,
>
> the problem is that during structure solution, many wrong
> paths may
> have to be followed until finally identifying the correct path.
>
> So the general answer to this kind of problem is: in some
> way, your
> parameterization of the experiment is wrong or incomplete.
>
> From what you write, data quality does not seem to be the
> problem.
> But: did XDS really integrate _all_ the reflections, or only a
> subset (say, every second reflection)?
>
> Check out
> http://strucbio.biologie.uni-____konstanz.de/ccp4wiki/index.____php/Refinement#what_can_go_____wrong_in_refinement.3F
> <http://strucbio.biologie.uni-__konstanz.de/ccp4wiki/index.__php/Refinement#what_can_go___wrong_in_refinement.3F>
>
>
> <http://strucbio.biologie.uni-__konstanz.de/ccp4wiki/index.__php/Refinement#what_can_go___wrong_in_refinement.3F
> <http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Refinement#what_can_go_wrong_in_refinement.3F>>
>
> If, after thorough attempts, you fail to find the solution,
> upload
> your current model, sequence and raw data frames to a
> Dropbox folder
> and post the link here - there may be people who succeed in
> processing the data nicely, or otherwise can identify the
> problem
> based on the data (rather than based on your description only).
>
> HTH,
>
> Kay
>
> Am 18.04.14 01:25, schrieb
> phenixbb-request at phenix-____online.org
> <mailto:phenixbb-request at phenix-__online.org>
> <mailto:phenixbb-request at __phenix-online.org
> <mailto:phenixbb-request at phenix-online.org>>:
>
>
> Date: Thu, 17 Apr 2014 16:25:00 -0700
> From: Yarrow Madrona<amadrona at uci.edu
> <mailto:amadrona at uci.edu> <mailto:amadrona at uci.edu
> <mailto:amadrona at uci.edu>>>
> To: PHENIX user mailing list<phenixbb at phenix-online.____org
> <mailto:phenixbb at phenix-__online.org
> <mailto:phenixbb at phenix-online.org>>>
>
> Subject: [phenixbb] Stalled refinement
> Message-ID:
>
>
> <__CAMHjG6bPE4q1xWidpE2VwFMJ9qLS____qjtLRuLMM1ef9vWBHBfZKg at mail.____gmail.com
> <http://gmail.com>
>
> <mailto:CAMHjG6bPE4q1xWidpE2Vw__FMJ9qLSqjtLRuLMM1ef9vWBHBfZKg at __mail.gmail.com
> <mailto:CAMHjG6bPE4q1xWidpE2VwFMJ9qLSqjtLRuLMM1ef9vWBHBfZKg at mail.gmail.com>>>
>
> Content-Type: text/plain; charset="utf-8"
>
>
> 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
> <https://www.dropbox.com/s/__2zsajl5o091k50r/CYP142A2-__032814_21_rf%20copy.pdf>
>
>
> <https://www.dropbox.com/s/__2zsajl5o091k50r/CYP142A2-__032814_21_rf%20copy.pdf
> <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
> <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
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> URL:<http://phenix-online.org/____pipermail/phenixbb/____attachments/20140417/e09ab4e4/____attachment.htm
> <http://phenix-online.org/__pipermail/phenixbb/__attachments/20140417/e09ab4e4/__attachment.htm>
>
> <http://phenix-online.org/__pipermail/phenixbb/__attachments/20140417/e09ab4e4/__attachment.htm
> <http://phenix-online.org/pipermail/phenixbb/attachments/20140417/e09ab4e4/attachment.htm>>>
>
> ------------------------------
>
>
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 4678 bytes
Desc: S/MIME Cryptographic Signature
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20140419/df052fa2/attachment-0001.p7s>
More information about the phenixbb
mailing list