April 2014 - phenixbb - phenix-online.org

Re: [phenixbb] Stalled refinement
by Yarrow Madrona 18 Apr '14

18 Apr '14

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(a)lbl.gov> wrote: > > What does triage say about translation NCS? > > > On Thu, Apr 17, 2014 at 4:25 PM, Yarrow Madrona <amadrona(a)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) 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 list >> phenixbb(a)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, Fax: 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(a)lbl.gov ][ 1-510-495-2506 > ] >

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DNA basepairing restraint refinement
by 李翔 18 Apr '14

18 Apr '14

Hi, I am working my low resolution data (6A) by MR and met a problem about DNA basepairing during refinement. I think so far everything looks OK except the bases flipped during the refinement. I added basepairing restraint for all bases, however, seems not help too much. Does anyone have experience on that? Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

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Stalled refinement
by Yarrow Madrona 17 Apr '14

17 Apr '14

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) 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

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geometry_regularization
by jp d 15 Apr '14

15 Apr '14

hi, the geometry_regularization option is gone from pdbtools in 1.8.4-1496 it looks like it works in 1.8.1, is that version ok to use ? thanks jpd

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homology models in sculptor
by "Weiergräber, Oliver H." 15 Apr '14

15 Apr '14

Hello, I am using phenix.sculptor for modification of a homology model in a challenging case of molecular replacement. The input model is complete (except at the termini), i.e. it exactly matches the target sequence as defined in the alignment file. In this scenario, are there any caveats to consider with individual options in sculptor? Specifically, a quick test seems to indicate that the Schwarzenbacher algorithm for side chain pruning does not work, i.e. not a single atom is removed from the model, whereas the alternative "similarity" option leads to deletion of a few hundred atoms. I'm using sculptor from the command line, and the log file indicates my input is interpreted correctly. Best regards Oliver ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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recovering the files from project directory
by Bishwa Subedi 14 Apr '14

14 Apr '14

Hi, I tried to use phenix in my personal computer for small checks and convenient use. I accidentally happened to make my project directory /user/XXX/Documents. Even though it was not the intended folder for running Phenix and later changed it to some other folders, I noticed that all my documents in that folder has disappeared (folder is empty). I do not see the files in trash folder as well. I assume this happened because of selecting documents as the project directory and phenix empties the folder before use, am I correct? If so is there any way to recover those files? Thanking you in advance. Best regards, Bishwa

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PhD position in Structural Biology in Norway
by Hans Petter Hersleth 11 Apr '14

11 Apr '14

Dear all, A 4-year PhD position in Structural Biology starting August 2014 is available at University of Oslo, Department of Biosciences, Section for Biochemistry and Molecular Biology. The position is funded by the Research Council of Norway and the University of Oslo. The project is dealing with different redox proteins (haem, flavin, iron-sulfur, and di-metal proteins) with a focus on flavodoxins, ferredoxins, ferredoxin/flavodoxin reductases and redox partner enzymes. The project is in the field of structural biology and biochemistry with a strong focus on protein crystallography in combination with other biochemical and biophysical methods including single-crystal spectroscopy. More information about the project, position and application procedure is found on the website: http://uio.easycruit.com/vacancy/1149343/96323?iso=no Applicants must hold a Master’s degree or equivalent in protein crystallography, structural biology, biochemistry or molecular biology. The successful applicant should have skills and experience in working with proteins. It would be advantageous with hands-on experience within topics like cloning, protein expression, purification, crystallisation, protein crystallography, spectroscopy, protein-protein interactions, enzyme kinetics, redox- and co-factor proteins and teaching. Candiates without a Master's Degree have until 30 June, 2014 to complete the final exam. Application deadline is 20th April 2014 through the website: http://uio.easycruit.com/vacancy/1149343/96323?iso=no For further information please contact: Dr. Hans-Petter Hersleth, (h.p.hersleth(a)ibv.uio.no) ---------------------------------------------------------------------------------------------- Hans-Petter Hersleth, PhD Department of Biosciences, University of Oslo Section for Biochemistry and Molecular Biology P.O.Box 1066 Blindern, NO-0316 Oslo, Norway http://www.mn.uio.no/ibv/personer/vit/hphersle/index.html -----------------------------------------------------------------------------------------------

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enforce ncs on ligand
by Garboczi, David (NIH/NIAID) [E] 10 Apr '14

10 Apr '14

I am not able to enforce ncs on two copies of a ligand. The ligand is largish, flavin-like. How do I use the information that the two ligands are identical in Phenix-refine. thanks, Dave

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fwd: 2nd Australian Advanced Methods in Crystallography Workshop
by Nathaniel Echols 10 Apr '14

10 Apr '14

---------- Forwarded message ---------- From: Sofia Caria <S.Caria(a)latrobe.edu.au> To: undisclosed-recipients:; Date: Wed, 9 Apr 2014 23:04:50 +0000 Subject: 2nd Australian Advanced Methods in Crystallography Workshop Dear all, The Australian Synchrotron is pleased to announce the *2nd Australian Advanced Methods in Crystallography Workshop*. This workshop will explore the state of the art in macromolecular crystallography. It will combine lectures on advanced topics in data collection, processing and structure determination with hands-on tutorials using both MX beamlines at the Australian Synchrotron. International experts will present their experience in solving crystal structures, model and ligand building, twinning and refinement. Associated with this workshop there will also be a day for Lipid Cubic Phase Crystallisation Satellite (LCP). Registration as part of the main event or separately is possible (see details in programme and registration). *Confirmed speakers: *Kay Diederichs, Harry Powell, Viviane Richter, Santosh Panjikar, Navraj Pannu, Daniele de Sanctis, Paul Adams, Joana Pereira, Paul Emsley, Tom Caradoc-Davies, David Aragão and Wei Liu. Workshop dates: 22-25th June 2014 Registration deadline: 22th May 2014 Website: https://events.synchrotron.org.au Contact: xtalworkshop2014(a)synchrotron.org.au Best regards, Sofia Caria (by the organising committee) *Organising committee:* Daniel Eriksson- Australian Synchrotron David Aragão - Australian Synchrotron Jade Forwood - Charles Sturt University Mihwa Lee - La Trobe University Sofia Caria - La Trobe University Stephanie Gras - Monash University

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AssertionError at asking for kicked maps
by Jorge Iulek 09 Apr '14

09 Apr '14

Dear all, It would be nice to have kicked maps for a structure I am working with now. When I set then to True, I get in my log: " ... shake map coefficients cycles: 0 1 2 3 4 5 6 7 8 9 shake f_model cycles: approx_equal eps: 1e-06 approx_equal multiplier: 10000000000.0 0.231506183818 approx_equal ERROR 0.235167389229 approx_equal ERROR Traceback (most recent call last): File "/usr/local/phenix-1.8.4-1496/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.8.4-1496/phenix/phenix/refinement/command_line.py", line 177, in run map_manger.write_files() File "/usr/local/phenix-1.8.4-1496/phenix/phenix/refinement/driver.py", line 1780, in write_files map_coeff_dataset=self.write_mtz_file(), File "/usr/local/phenix-1.8.4-1496/phenix/phenix/refinement/driver.py", line 1766, in write_mtz_file pdb_hierarchy=self.refine_object.model.pdb_hierarchy()) File "/usr/local/phenix-1.8.4-1496/cctbx_project/mmtbx/maps/__init__.py", line 515, in __init__ pdb_hierarchy = pdb_hierarchy) File "/usr/local/phenix-1.8.4-1496/cctbx_project/mmtbx/maps/__init__.py", line 439, in map_coefficients_from_fmodel map_type = params.map_type).map_coefficients File "/usr/local/phenix-1.8.4-1496/cctbx_project/mmtbx/maps/__init__.py", line 650, in __init__ assert approx_equal(fmodel.r_work(), fmodel_dc.r_work()) AssertionError " I see a previous problem like this at http://www.phenix-online.org/pipermail/phenixbb/2009-July/013517.html , but I cannot find a follow up concerning how to solve it. I am using the latest stable version, phenix-1.8.4-1496 , under openSuSE 12.3. When I set kicked maps to false, everything goes fine. Can this be solved? Also, a point to a former version that can "kick" would be enough. Thanks, Jorge

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