March 2013 - phenixbb - phenix-online.org

Refinement of B-factors at low resolution
by Florian Brückner 25 Mar '13

25 Mar '13

Dear all I am refining a structure at 3.2 A with phenix.refine using automatic optimization of target weights, solved by molecular replacement with a 2.1A structure of the same crystal form. Rwork=26%, Rfree=28%. I use individual atomic B-factor refinement. The obtained distribution of B-factors after refinement looks reasonable and quite similar to the distribution in the higher resolution model, which I suppose would be expected, since it is the same crystal form. However, the average B-factor does not change substantially, i.e. if I start with the B-factors from the high resolution model (average B-factor around 32 A**2) after 6 macrocycles the average B-factor is still around 32 A**2. If I set all B-factors to the Wilson B-factor determined by phenix.refine (66 A**2), after 6 macrocycles the distribution of B-factors looks again very similar to the high resolution MR model, but the average B-factor is still around 65 A**2. What should I make of this? Is this an expected behavior at this resolution, i.e. the fact that the absolute values of B-factors cannot be determined during refinement, although a reasonable distribution can be obtained as judged by plotting average B-factors vs. residue#? Since the average B-factor does not change much during refinement, which average B-factor should I start refinement with to end up with reasonable absolute values? I have manually determined the Wilson B-factor from the linear part of the Wilson plot (4.5-3.2 A) to be 97 A**2. This seems high to me. Would that be expected for the given resolution, given that the 2.1A structure of the same crystal form has 32 A**2? I should add, that there is not a substantial effect of the average refined B-factor on Rfree. Thanks for any comments or suggestions. Best regards Florian ------------------------------------------------------------- Dr. Florian Brückner Laboratory of Biomolecular Research (LBR) OFLG/102 Paul Scherrer Institut CH-5232 Villigen PSI Switzerland Tel.: +41-(0)56-310-2332 Email: florian.brueckner(a)psi.ch

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molecular replacemnt problem
by Appu kumar 24 Mar '13

24 Mar '13

Dear members, I am doing a molecular replacement of a transcription factor whose ligand binding structure(24000 Da) is available in PDB but not for the DNA binding(13000 Da). When i am searching for the two copies from ligand binding domain as a template model, i am getting very good solution but i am not getting any density for the DNA binding domain to build up in density. The space gorup is P 1 21 1 (4) and unit cell parameters are Unit Cell: 57.43 69.36 105.99 90.00 90.00 90.00. Please guide me how to get the complete model structure. Table below show the matthews statistics For estimated molecular weight 37000. Nmol/asym Matthews Coeff %solvent P(2.20) P(tot) _____________________________________________________________ 1 5.71 78.46 0.00 0.01 2 2.85 56.91 0.62 0.70 3 1.90 35.37 0.37 0.29 4 1.43 13.82 0.00 0.00 _____________________________________________________________ The phaser molecular replacement gives the following table. istogram of relative frequencies of VM values ---------------------------------------------- Frequency of most common VM value normalized to 1 VM values plotted in increments of 1/VM (0.02) <--- relative frequency ---> 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 | | | | | | | | | | | 10.00 - 8.33 - 7.14 - 6.25 - 5.56 - 5.00 - 4.55 - 4.17 - 3.85 -- 3.57 --- 3.33 ------ 3.12 ---------- 2.94 **************** (COMPOSITION*1) 2.78 ----------------------- 2.63 -------------------------------- 2.50 ----------------------------------------- 2.38 ------------------------------------------------ 2.27 -------------------------------------------------- 2.17 ----------------------------------------------- 2.08 -------------------------------------- 2.00 -------------------------- 1.92 --------------- 1.85 ------- 1.79 --- 1.72 - 1.67 - 1.61 - 1.56 - 1.52 - 1.47 * (COMPOSITION*2) 1.43 - 1.39 - 1.35 - 1.32 - 1.28 - 1.25 - TABLE : Cell Content Analysis: SCATTER :N*Composition vs Probability:0|3x0|1:1,2: $$ N*Composition Probability $$ loggraph $$ 1 0.306066 2 0.00141804 $$ Most probable VM for resolution = 2.27817 Most probable MW of protein in asu for resolution = 92664.2 I have initially indexed the data in C2221 but Rfree was not decreasing so i reindexed the data in data in P121 space group keeping the Rfree flag of C2221. While analysing the symmetry mates , i found large space but no density. structure of Ligand binding domain is almost identical with 90% identity in sequence. I am stuck with this problem and don't know how to process further. I run the phenix.xtriage to evaluate the twining but it suggest no twining. When i reindex from C2221 to P21, the completeness of data reduced from 95 % to 35% whereas the map is very good and Rwork and Rfree are 26/31 for 2.2 resolution. I do not understand why the completeness of data reduced so much on reindexing. please Can anyone explain this phenomenon. Please give me your valuable suggestion. I will appreciate your effort. Thank you

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one or more errant TER cards
by jp d 20 Mar '13

20 Mar '13

hi, i am trying to refine using a reference model and keep getting this error *** Adding Reference Model Restraints *** Sorry: chain ' ' in start.pdb contains one or more errant TER cards. Please remove and try again i've tried various things including removing all the TER lines my models (reference and working) has many chains identified by segid's any suggestions ? thanks jpd

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install on ubuntu 12.04?
by Alastair Fyfe 20 Mar '13

20 Mar '13

Hi, I've installed previous phenix builds on ubuntu without problem, but with both 1.8.1-1168 and dev-1269 installers on 12.04, the command "./install --prefix=/home/afyfe" ends with "Error configuring: see /home/afyfe/phenix-installer-dev-1269/build-binary/intel-linux-2.6/svr/log/binary.log for details" and the tail of the binary.log file suggests: -- Creating files in build directory: "/home/afyfe/phenix-dev-1269/build/intel-linux-2.6" dispatcher_include_template.sh dispatcher_head.sh Please re-configure from scratch your cctbx_build:cd cctbx_build; /your/path/to/python ../cctbx_project/libtbx/configure.py [options] [modules] --- I don't see a cctbx_build directory under either the installer or destination directories. Any clues/suggestions? many thanks, Alastair

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International Conference on Structural Genomics - Structural Life Science, Sapporo, Japan, July 29-Aug 1, 2013
by Terwilliger, Thomas C 19 Mar '13

19 Mar '13

Dear Colleagues: On behalf of the organizing committee of the International Conference on Structural Genomics 2013 – Structural Life Science – (ICSG2013-SLS), we cordially welcome you to the conference, to be held in Sapporo, Hokkaido, Japan, July 29th – August 1st, 2013. ICSG2013-SLS is intended to provide an overview for the most recent developments in Structural Genomics and its impact on research in biology, medicine and disease, and to foster international collaboration among researchers. You can see all the details of the conference at: http://www.c-linkage.co.jp/ICSG2013 . Registration for the conference is now open. The scientific topics covered in ICSG2013-SLS include the wider life science research fields with particular attention to drug discovery (small molecules and biopharmaceuticals), biotechnology and industrial issues while keeping strength in the high-throughput technologies and integration of hybrid methods. These technologies are now leading to the new field of “Structural Life Science”. ICSG2-13-SLS is partially supported by the Grant-in-Aid for Scientific Research on Innovative Areas; “Structural Cell Biology”, “Intrinsically Disordered Protein” and “Transient Macromolecular Complexes”, from Ministry of Education, Culture, Sports, Science and Technology (MEXT) . In order to widen the opportunity to young and enthusiastic fellows to study more, we have organized several satellite workshops before ICSG2013- SLS. The topics will include “Small molecule screening”, “Automation of X-ray Structure Determination”, “Cell-free Protein Production”, “Automated NMR methods”, "Eukaryotic expression", “Interaction analyses" and "Bioinformatics”. We hope you also find the satellite workshops are informative and productive. The conference will be held in Keio Plaza Hotel Sapporo, in walking distance of Hokkaido University's main campus and Sapporo station. The summer in Sapporo is a great time to stay and enjoy the cool summer night of Japan. We are looking forward to welcoming you to Sapporo in the summer of 2013. Sincerely yours, Katsumi Maenaka, Ph.D. Chair, International Conference on Structural Genomics 2013 -Structural Life Science- (ICSG2013-SLS) Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Japan Soichi Wakatsuki Chair of Program Committee, ICSG2013-SLS Photon Science, SLAC National Accelerator Laboratory Department of Structural Biology School of Medicine Stanford University

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MR_rosetta and disulphides
by Morten Groftehauge 18 Mar '13

18 Mar '13

Hi guys, Phenix version 1323 Rosetta version 3.4 I try to run phenix.mr_rosetta rosetta_command="-MR::disulf 129:411 228:281 279-615" mr_rosetta_228.eff but I get the following error in rebuild.log ERROR: Option matching -MR:disulf not found in command line top-level context I lifted the rosetta_command directly from the Version Documentation. Any clues as to why this doesn't work? Sincerely, -- Morten K Grøftehauge, PhD Pohl Group Durham University

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Tutorial of low resolution data?
by 李翔 17 Mar '13

17 Mar '13

Hi everyone, I will work on some low resolution data but have very little experience. (Data are about 4 A to 8 A) Does anyone know where I could find a tutorial for low resolution data please? It is best to work with Phenix, other software is fine. MIR or SAD or MR method will be appreciated and it is very helpful if the tutorial can talk about some details of the data processing. Cheers, Frank

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Phenix DEN-twin-refinement
by Ethayathulla A.S 15 Mar '13

15 Mar '13

hi all I want to do DEN twin-refinement using phenix. For my data phenix.DEN works better than CNS DEN. I want to DEN with twinning. Is there script for adding twinning operator for DEN refinement in phenix phenix.den_refine model.pdb data.mtz den.reference_file=reference.pdb Thank you Abdul --

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Re: [phenixbb] problems installing latest phenix on mac osx lion
by Alejandro Buschiazzo 15 Mar '13

15 Mar '13

Thanks Nat! read your message a bit later (I think I need to change from the digest format, so I receive each message as it comes), looking at http://phenix-online.org/pipermail/phenixbb/2013-March/thread.html Actually, your suggestion worked all right. (and by sourcing the phenix_env.sh as you point out, it's actually the same as the command line -installer of course) Don't know why the errors appeared before, but in any case, now it's running fine. Thank you for your help Alejandro > Not sure what's going on here - I will check it out today. There's > one more option however that should be the safest: did you try the > graphical installer yet? The destination can't be changed, but you > can still use the command line if you want by doing this: > > source /Applications/PHENIX-1.8.2-1309/Contents/phenix-1.8.2-1309/phenix_env.sh > > (or the csh equivalent) > > But I will see if there's an explanation for these errors. > > -Nat On Tue, Mar 12, 2013 at 4:26 AM, Alejandro Buschiazzo <alebus at pasteur.edu.uy <http://phenix-online.org/mailman/listinfo/phenixbb>> wrote: >/ I 'm trying to install phenix 1.8.2-1309 on a Macbook Pro (os x 10.7.5). />/ />/ First tried the binary installer proposed (which is indicated for os x />/ 10.6.7) />/ It didn't work, ending with "fix_mac_python: caught error - exiting." />/ />/ I spotted in the bb that this could've happened because the downloaded />/ installer was somehow corrupted, tried downloading it again, but same />/ result. />/ />/ Tried then the source installer: everything OK - except for wxPython, giving />/ this error />/ />/ WXPYTHON: />/ Using wxOSX_Cocoa build of wxPython 2.9 alpha version />/ />/ building wxPython-src-2.9.4.1 />/ ERROR: installation of wxosx_cocoa failed />/ />/ ERROR: installation of wxpython failed />/ />/ ...now I can work with command lines, but the GUI won't work of course. />/ />/ Your help is appreciated />/ />/ Alejandro />/ />/ />/ -- />/ Alejandro Buschiazzo, PhD />/ Research Scientist />/ Unit of Protein Crystallography />/ Institut Pasteur de Montevideo />/ Mataojo 2020 />/ Montevideo 11400 />/ URUGUAY />/ Phone: +598 25220910 int. 120 />/ Fax: +598 25224185 />/ http://www.pasteur.edu.uy/pxf/ -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

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Fwd: 4th Edition of the ISBC2013
by Nathaniel Echols 15 Mar '13

15 Mar '13

---------- Forwarded message ---------- From: Jose A. Gavira <gavirius(a)gmail.com> Date: Thu, Mar 14, 2013 at 11:20 AM Subject: 4th Edition of the ISBC2013 Dear Colleague, The Laboratory of Crystallographic Studies is pleased to announce the 4th International School on Biological Crystallization (ISBC2013), to be held in Granada (Spain) during May 26-31, 2013. ISBC2013 is intended for postgraduate/postdoctoral students and research scientists from industrial and academic backgrounds. The International School will provide five days of lectures, posters and practical demonstrations focused on the fundamentals of crystallization from solution and their applications to the field of crystallization of biological materials, including biological macromolecules, biominerals and biomimetic materials. One day will be fully devoted to case studies on the crystallization of membrane proteins, viruses and large macromolecular complexes. For more information, please visit http://www.isbcgranada.org/<http://www.linkedin.com/redirect?url=http%3A%2F%2Fwww%2Eisbcgranada%2Eorg%2…> . Best regards, ISBC2103 Organizing Committee --- Gavi http://isbcgranada.org/

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