- phenixbb - phenix-online.org

Phenix-rosetta refinement problems
by Oliver Clarke 05 May '14

05 May '14

Hi all, I am struggling a little to get Rosetta and phenix to play happily with one another (I’d like to use the phenix.rosetta_refine module). I am currently using the latest nightlies of phenix (1.9-1690) and rosetta (2014.16.56682), and I run into errors (reproduced below) when attempting to build the phenix-rosetta interface. Does anyone have any insights as to how to fix this problem, or suggestions as to which pair of phenix and rosetta versions are known to be compatible with one another? Many thanks, Oliver. Errors while building phenix-rosetta interface: <snip> chdir(tempdir_.c_str()); src/core/scoring/cryst/PhenixInterface.cc:375:13: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(".."); ^ src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::initialize_target_evaluator(const core::pose::Pose&, std::string)': src/core/scoring/cryst/PhenixInterface.cc:949:25: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(tempdir_.c_str()); ^ src/core/scoring/cryst/PhenixInterface.cc:1075:13: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(".."); ^ src/core/scoring/cryst/PhenixInterface.cc: In member function 'std::string core::scoring::cryst::PhenixInterface::calculateDensityMap(core::pose::Pose&, bool)': src/core/scoring/cryst/PhenixInterface.cc:1095:25: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(tempdir_.c_str()); ^ src/core/scoring/cryst/PhenixInterface.cc:1104:13: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(".."); ^ g++ -o build/src/release/linux/3.11/64/x86/gcc/4.8/python/core/scoring/MinimizationGraph.os -c -std=c++98 -isystem external/boost_1_55_0/ -isystem external/include/ -isystem external/dbio/ -pipe -ffor-scope -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/MinimizationGraph.cc cc1plus: all warnings being treated as errors scons: *** [build/src/release/linux/3.11/64/x86/gcc/4.8/python/core/scoring/cryst/PhenixInterface.os] Error 1 scons: building terminated because of errors.

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Post Doctoral Positions in Membrane Protein Structure and Function at the National Institutes of Health (NIH)
by Anirban Banerjee 03 May '14

03 May '14

Dear all, Please circulate to those who may be interested - The research group of Dr. Anirban Banerjee at the National Institutes of Health (NIH) is seeking candidates for postdoctoral fellows . The broad interests of the lab are in membrane protein structure and function. We will combine structural techniques such as macromolecular crystallography with biophysical and biochemical methods such as reconstitution based biochemistry, electrophysiology together with synthetic chemistry to investigate the structural bases of the mechanisms of a number of membrane proteins. The lab has state-of-the-art equipment and facilities. We have dedicated periodic access to the 22-ID beamline at the APS, for crystallographers at the NIH. The DC Metro area is a wonderful place to live, the weather is pleasant and is a vibrant international community. In terms of scientific opportunities, the NIH is absolutely unique in bringing scientists from a virtually all corner of biomedical sciences in one campus. The Cell Biology and Metabolism program is part of the National Institute of Child Health and Human Development (NICHD). Our lab also has an affiliation to the National Institute of Neurological Disorders and Stroke (NINDS). The candidates should hold a Ph. D. degree, must be motivated and a have strong background in biochemistry or structural biology. Experience with protein expression, purification and biochemical characterization is required. Prior experience in membrane protein biochemistry or insect/mammalian expression systems will be added advantages. Interested candidates can send an e-mail to anirban.banerjee(a)nih.gov with a CV and a summary of previous research experience and future interests. Disclaimers: The NIH is dedicated to building a diverse community in its training and employment programs and this position is subject to a background investigation. Thanks very much. Best, Anirban

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Partial Model for Mol Rep.
by Yuri 02 May '14

02 May '14

Hi Everyone, I am trying to solve a structure (to 2.15 Ang). I am pretty sure about one of the domains fold but it only covers residues 26-250 while the whole protein is 470aa. Could I attempt to use this small part of the protein to phase my data and hopefully start building? How is that handled in PHENIX? ps. Selenomet protein will be expressed soon.. -- Yuri Pompeu, Ph.D.

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refining two chains into same density
by Scott Horowitz 02 May '14

02 May '14

I have a strange case where I think there are two separate protein chains that are partially occupying the same spot (i.e. two proteins:one binding site=half of each bound). I'd really like to try to simultaneously refine both chains at partial occupancy into this density, but when I tried this (not surprisingly) it terminated because there were some overlapping atomic coordinates between the two chains. Is there a way to work around this? Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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phenix start-up error !
by abhisek Mondal 01 May '14

01 May '14

hi. I have recently installed phenix-1.8.4 in my lab's RHEL work-station using './install' command. When i try to use 'phenix command' , the cursor of the terminal goes on blinking for almost hours, before opening the gui. Is there any way to avoid such long start-up time.! thank you. -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics* *Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA*

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problem with MR
by Subhani Bandara 30 Apr '14

30 Apr '14

Hi all, I am trying to solve the structure of 7 KDa protein with a cubic space group at 1.35A resolution with Phaser-MR. It gives the error massage saying "The composition you have entered has a protein/nucleic acid content of 300.3%, which is impossible. Decrease your composition" and stops. This appears even if I give one chain as search model and say there is only one component copy. How can I fix this. Thanks Subhani

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CASP 11: Call for targets to assess the state of the art in protein structure modeling
by Torsten Schwede 29 Apr '14

29 Apr '14

Summary: CASP is soliciting target proteins for structure prediction - specifically proteins with new folds, membrane proteins, disordered proteins, oligomers, complexes, and multi-domain proteins. Call for targets: ============= As many of you know, CASP (Critical Assessment of Structure Prediction) has been assessing the state of the art in modeling protein structure from sequence since 1994, running a community experiment once every two years. In these experiments, information on soon to be solved structures is collected from the experimental community, and the sequence data are passed to the structure modeling community so that blind predictions of structure can be collected and assessed (1). Over that period CASP has seen enormous progress in the quality of modeled structures (2), but many problems remain. CASP is only possible because of the generous participation of the experimental community in providing the modeling targets (3). The prediction season for the next full biannual experiment, CASP 11, begins May 1, and so we are now asking for your help in reaching our goal of releasing at least varied 100 targets in a the three-month period. We need all sorts of targets, spanning the categories below: 1. (More than ever) novel folds and membrane protein targets. Even with the extended collection season provided by CASP ROLL, there will be still a shortage. There are some interesting methods developments for ab initio modeling, and it is important to be able to decisively evaluate their effectiveness. 2. Oligomers, complexes, and multi-domain proteins: This round, CASP has entered collaboration with CAPRI for specifically assessing the accuracy of predictions of protein-interactions and relative domain orientation. 3. Targets containing significant amounts of disordered structure, so as to test the ability of methods to identify these regions. We are especially interested in targets where disorder has been directly characterized experimentally, e.g. by NMR. 4. A diversity of comparative modeling targets. Cases where there is fairly high sequence identity (30-50%) between the target structure and an available template are valuable for testing the degree to which model accuracy can approach that of experiment, particularly in functionally critical regions. Cases with lower sequence identity to template, right down to undetectable, are valuable for testing the ability of the methods to detect remote homologs, to overcome challenging alignment difficulties, to make use of multiple templates, and to build regions of the structure not obviously available from a template. 5. Some targets will also be used to test methods of structure refinement. In these cases, the best model received for a target will be released to the refinement community, who will subsequently submit new models. This too is an area where there have been some exciting developments in the last year, so we are hoping for significant progress. Refinement targets are selected based on the nature of the errors in the initial models. Because of the extended process, these targets need to be available for longer before release of the experimental structure. Procedure ========= For those of you who have not provided targets to CASP before, the procedure is simple. There are three ways to submit targets: (1) Go the target submission web page and fill in the easy form; (2) When you submit your co-ordinates to the PDB, tick the 'CASP HOLD' box, automatically setting up a target entry; (3) Send an email the prediction center with details. If you have queries, there is very experienced prediction center staff to deal with them. The key thing is timing: We need a window of at least four weeks between receiving information about a target and the release of your experimental structure. A longer window - up to eight weeks - is often useful, for example so that a target can be used to test refinement methods, but is not essential (note that using the PDB target submission route automatically selects eight weeks). We don't need your experimental structure in advance of its release by the PDB, provided that will happen by the end of August. Please consult the target submission page for more details: http://www.predictioncenter.org/casp11/targets_submission.cgi There are already many prediction teams signed for CASP 11, and so any targets provided will receive plenty of attention. If you have a suitable target now, we are ready to receive it. If new targets come up before mid of July, we would also love to have them. (After July, we will continue with CASP ROLL for novel folds, disordered proteins, and membrane proteins). So please get in touch whenever a suitable opportunity arises, and help improve modeling methods. Thanks, CASP organizing committee John Moult, IBBR, University of Maryland, USA Anna Tramontano, University of Rome, Italy Krzysztof Fidelis, University of California, Davis, USA Andriy Kryshtafovych, University of California, Davis, USA Torsten Schwede, SIB & Biozentrum University of Basel, Switzerland References ========= 1. Moult, John; Fidelis, Krzysztof; Kryshtafovych, Andriy; Schwede, Torsten; Tramontano, Anna (2014). Critical assessment of methods of protein structure prediction (CASP) - round X. Proteins, 82(S2), 1-6. 2. Kryshtafovych A, Fidelis K, Moult J. (2014) CASP10 results compared to those of previous CASP experiments. Proteins. 82 (S2):164-174. 3. Kryshtafovych, Andriy; Moult, John; Bales, Patrick; Bazan, J Fernando; Biasini, Marco; Burgin, Alex; Chen, Chen; Cochran, Frank V; Craig, Timothy K; Das, Rhiju; Fass, Deborah; Garcia-Doval, Carmela; Herzberg, Osnat; Lorimer, Donald; Luecke, Hartmut; Ma, Xiaolei; Nelson, Daniel C; van Raaij, Mark J; Rohwer, Forest; Segall, Anca; Seguritan, Victor; Zeth, Kornelius; Schwede, Torsten (2014). Challenging the state-of-the-art in protein structure prediction: Highlights of experimental target structures for the 10(th) Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. Proteins, 82(S2), 26-42. Get in touch: casp(a)predictioncenter.org More information: http://www.predictioncenter.org/casp11/ Submit a target: http://www.predictioncenter.org/casp11/targets_submission.cgi

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MRage problem
by Appu kumar 27 Apr '14

27 Apr '14

Hello all, I am trying to find the molecular replacement for a protein of 75kDa at 6.1A, Space group is I422. MRage gave me a good solution once. But when i repeated the MRage with same parameters, it is not giving me the same solution and giving me wrong solution. Would you please help me in getting the solution which i got once. I have the information about the euler anglle. I will be highly grateful for the help. Thank you Appu

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Low resolution refinement
by Appu kumar 26 Apr '14

26 Apr '14

Hello All, I want to refine the low resolution structure (6.5A). It is a membrane protein and we are able to phase it. It will be great help if any one can guide me how to proceed further with the refinement. People uses Phenix to refine low resolution structure, so phenix is really a good program to proceed for refinement against low resolution. Thank in advance Appu

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Build Phenix from Source Code
by Chen Zhao 25 Apr '14

25 Apr '14

Dear all, I would like to try phenix.rosetta_refine and it is said in the online tutorial that the phenix should be built from source code in linux. However I ran into some errors, and I am too far from a linux export to figure it out. I am using Debian Wheezy with kernel 3.2.0-4-amd64. I download the source installer (phenix-installer-1.9-1683-source.tar) and run the installer as: # ./install --prefix=/usr/local/src --nproc=8 --no-gui (it seems from README-DEV that there is no --python-shared flag as described in the online tutorial) After while, I receive the following error message: ************************************************************************************************************************* Installing Imaging... log file is /workspace/setup/phenix-installer-1.9-1683/build-source/intel-linux-2.6-x86_64/cz-thinkpadw530-debian/tmp/Imaging_install_log getting package Imaging-1.1.7.tar.gz... using /workspace/setup/phenix-installer-1.9-1683/base/Imaging-1.1.7.tar.gz Traceback (most recent call last): File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install", line 9, in <module> install_cctbx_base.installer(args=sys.argv, log=sys.stdout) File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 95, in __init__ self.build_cctbx_dependencies() File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 134, in build_cctbx_dependencies self.build_imaging() File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 349, in build_imaging confirm_import_module="Image") File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 325, in build_python_module_simple log=pkg_log) File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 150, in call return call(args, log=log) File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/installer_utils.py", line 51, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/usr/local/src/phenix-1.9-1683/build/intel-linux-2.6-x86_64/base/bin/python setup.py build ' failed with exit code 1 FATAL ERROR: aborting installation. ************************************************************************************************************************* I looked into Imaging_install_log, and at the end, I have the following errors: ************************************************************************************************************************* /usr/bin/ld: /usr/local/lib/libpython2.7.a(abstract.o): relocation R_X86_64_32S against `_Py_NotImplementedStruct' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libpython2.7.a: could not read symbols: Bad value collect2: error: ld returned 1 exit status error: command 'gcc' failed with exit status 1 *************************************************************************************************************************** Could anybody help me out? Thank you so much, Chen

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Re: [phenixbb] Build Phenix from Source Code
by Chen Zhao 25 Apr '14

25 Apr '14

I switched to version 1.8.4-1496 and this time the same error didn't occur. Also --python-shared/--with-rosetta flag works. But I ran it as # ./install --prefix=/usr/local/src --nproc=8 --no-gui --phython-shared then regenerate the dispatchers by running libtbx.refresh as shown in the message after installation. However, the installation is not complete, and if I source phenix_env.sh, the error message as below will show up: *************************************************************************************************************** bash: /usr/local/src/phenix-1.8.4-1496/bin/machine_type: No such file or directory bash: /usr/local/src/phenix-1.8.4-1496/bin/machine_version: No such file or directory bash: /usr/local/src/phenix-1.8.4-1496/bin/find-installation: No such file or directory *************************************************************************************************************** What else should I run to complete building phenix? PS. Because the first time I didn't append --python-shared flag, I build it again after deleting the original directory. I guess there might be files elsewhere that are changed, since I didn't have this error the first time. Thanks a lot, Chen On Thu, Apr 24, 2014 at 11:10 PM, Chen Zhao <c.zhao(a)yale.edu> wrote: > OK, thank you for your suggestion! I will do that. But as a perfectionist, > I will try to finish with the installation. I later found that the flag is > --with-rosetta but not --python-shared... I have to build it again... > Crying... > > Best, > Chen > > > On Thu, Apr 24, 2014 at 11:06 PM, Meng, Wuyi <wuyi.meng(a)yale.edu> wrote: > >> Sbgrid version means the version compiled by sbgrid (on 130.132.25.142and other cbic Mac Pros). The Mac Pro runs 2x fast than csb and yale hpc >> computers of same phenix refinement, they have 8 cores too. Rosetta runs >> usually take days to weeks to finish, it is wise to do it on yale hpc >> cluster. >> >> Wuyi, >> >> On Apr 24, 2014, at 10:49 PM, Chen Zhao <c.zhao(a)yale.edu> wrote: >> >> Dear Wuyi, >> >> Thank you for your warm help as always! But actually SBGrid is not >> "installed" in this machine (don't laugh, it is my laptop...) Do you mean >> phenix-1.8.4-1496 when saying the SBGrid version? I did try this version >> after you mentioned and at least it passed the step that gave me the error >> before. I will wait and see how the compilation goes. And if this works, >> hopefully there will be no error when running >> rosetta.build_phenix_interface. I will try the one on130.132.25.142 if >> nothing works. >> >> Thank you so much again! >> >> Good night, >> Chen >> <130.132.25.142> >> >> >> On Thu, Apr 24, 2014 at 10:35 PM, Meng, Wuyi <wuyi.meng(a)yale.edu> wrote: >> >>> phenix.rosetta_refine should work on 130.132.25.142 according to >>> following statement from sbgrid: >>> >>> Linux 64-bit We have installed and configured nightly versions >>> of Phenix and Rosetta to support the newly announced Phenix-Rosetta >>> refinement mentioned in Nature Methods. These experimental versions are not >>> the default, so you'll need to add version >>> overrides in your ~/.sbgrid.conf file: P HE N I X _ X = n i g h t l y R >>> O S E T T A _ X = n i g h t l y You can refresh your memory for setting >>> version overrides on our website. These new features are only available on >>> 64-bit Linux at this time. Phenix >>> generally has very good support for OS X, but Macs >>> seem to be a second tier platform for the Rosetta >>> developers. >>> >>> Wuyi, >>> >>> > On Apr 24, 2014, at 10:14 PM, Chen Zhao <c.zhao(a)yale.edu> wrote: >>> > >>> > Dear all, >>> > >>> > I would like to try phenix.rosetta_refine and it is said in the online >>> tutorial that the phenix should be built from source code in linux. However >>> I ran into some errors, and I am too far from a linux export to figure it >>> out. I am using Debian Wheezy with kernel 3.2.0-4-amd64. I download the >>> source installer (phenix-installer-1.9-1683-source.tar) and run the >>> installer as: >>> > >>> > # ./install --prefix=/usr/local/src --nproc=8 --no-gui (it seems from >>> README-DEV that there is no --python-shared flag as described in the online >>> tutorial) >>> > >>> > After while, I receive the following error message: >>> > >>> > >>> ************************************************************************************************************************* >>> > Installing Imaging... >>> > log file is >>> /workspace/setup/phenix-installer-1.9-1683/build-source/intel-linux-2.6-x86_64/cz-thinkpadw530-debian/tmp/Imaging_install_log >>> > getting package Imaging-1.1.7.tar.gz... >>> > using >>> /workspace/setup/phenix-installer-1.9-1683/base/Imaging-1.1.7.tar.gz >>> > Traceback (most recent call last): >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install", >>> line 9, in <module> >>> > install_cctbx_base.installer(args=sys.argv, log=sys.stdout) >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", >>> line 95, in __init__ >>> > self.build_cctbx_dependencies() >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", >>> line 134, in build_cctbx_dependencies >>> > self.build_imaging() >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", >>> line 349, in build_imaging >>> > confirm_import_module="Image") >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", >>> line 325, in build_python_module_simple >>> > log=pkg_log) >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", >>> line 150, in call >>> > return call(args, log=log) >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/installer_utils.py", >>> line 51, in call >>> > raise RuntimeError("Call to '%s' failed with exit code %d" % >>> (args, rc)) >>> > RuntimeError: Call to >>> '/usr/local/src/phenix-1.9-1683/build/intel-linux-2.6-x86_64/base/bin/python >>> setup.py build ' failed with exit code 1 >>> > FATAL ERROR: aborting installation. >>> > >>> ************************************************************************************************************************* >>> > >>> > I looked into Imaging_install_log, and at the end, I have the >>> following errors: >>> > >>> > >>> ************************************************************************************************************************* >>> > /usr/bin/ld: /usr/local/lib/libpython2.7.a(abstract.o): relocation >>> R_X86_64_32S against `_Py_NotImplementedStruct' can not be used when making >>> a shared object; recompile with -fPIC >>> > /usr/local/lib/libpython2.7.a: could not read symbols: Bad value >>> > collect2: error: ld returned 1 exit status >>> > error: command 'gcc' failed with exit status 1 >>> > >>> *************************************************************************************************************************** >>> > >>> > Could anybody help me out? >>> > >>> > Thank you so much, >>> > Chen >>> > >>> > _______________________________________________ >>> > phenixbb mailing list >>> > phenixbb(a)phenix-online.org >>> > http://phenix-online.org/mailman/listinfo/phenixbb >>> > >>> > >>> > The information in this e-mail is intended only for the person to whom >>> it is >>> > addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> > contains patient information, please contact the Partners Compliance >>> HelpLine at >>> > http://www.partners.org/complianceline . If the e-mail was sent to >>> you in error >>> > but does not contain patient information, please contact the sender >>> and properly >>> > dispose of the e-mail. >>> >> >> >

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HELP. semelno met refinement not working.
by Kenneth A. Satyshur 24 Apr '14

24 Apr '14

When I refine my seleno met residues in Phenix (1.8.4-1496) ALL my MSE are restrained to ONE conformer, in coot terms ptp #11 with a Chi 1 of 60 deg. This happens at the start of the second cycle when it does 'rsrl'. I can watch it happen in coot. POP! There is goes. Some of the MSE are in this conformation, but not all of them. This refinement is wrong, so how do I correct it? thanks kas -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207

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BCA/CCP4 Summer School in Protein Crystallography at Diamond
by Airlie McCoy 24 Apr '14

24 Apr '14

Applications are now open for the BCA/CCP4 Summer School in Protein Crystallography to be held at Diamond (UK) from Tuesday 26th August to Sunday 31st August 2014. Applications close 1st May 2014. References are due by 8th May 2014. The BCA/CCP4 Protein Crystallography Summer School is intended for students and researchers new to crystallography. Its dual aims are to provide comprehensive training in crystallography and to promote best practise within the British crystallographic community. The lectures cover the gamut of techniques required for a structure solution, from protein expression through to structure validation. Intensively supervised computer tutorials enable students to relate the theory presented in the lectures to practice. Although CCP4 programs will primarily be used in these tutorials, the aim will be to approach crystallographic questions in a software-agnostic manner. There will also be a crystal manipulation and cooling workshop. Note that the course is scheduled during Diamond synchrotron downtime, so there will not be active data collection at the Diamond beamlines. For more information on eligibility, cost, and applications see: http://www.diamond.ac.uk/Home/Events/BCA-Summer-School.html Application form: http://extranet2.diamond.ac.uk/ISV/EventWidget/BCA/ApplicationsForm.aspx

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inputing tNCS into phenix?
by Yarrow Madrona 23 Apr '14

23 Apr '14

Hello, I recently posted a question about stalled R-factors and and obtained excellent help resulting in the realization that I have tNCS even though it is not picked up by X-triage. I know the transformation matrix of one molecule onto another but I am not sure how to input this into phenix (both the translation and the rotation) to improve refinement. Is there a way to do this? I'm sorry if this has already been covered. -Yarrow

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Trouble Refining Ligand in Phenix
by Chris Fage 22 Apr '14

22 Apr '14

Hi Everyone, I am trying to refine a structure with a phosphorylated amino acid. After refining in Phenix, the Fo-Fc density (green) overlaps the 2Fo-Fc density for all atoms of the derivatized amino acid in Coot, almost as if I had not built in the residue. I am loading a .cif for the derivative when I run phenix.refine. I have also tried ReadySet, but when I click the "Run in phenix.refine" button, I see the message Error interpreting command line argument as parameter definition: "refine_65-coot-2.metal.edits" RuntimeError: Unexpected end of output. Am I just seeing noise, or is Phenix not actually refining this portion of the model? I would appreciate any suggestions. Best, Chris

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Saenger class in nucleic acids
by Chen Zhao 22 Apr '14

22 Apr '14

Dear all, Could anybody point me to a reference for the saenger_class and leontis_westhof_class in nucleic acids? I just failed to find it in the long reference list in the phenix.refine online tutorial. Thanks a lot in advance, Chen

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inputing tNCS into phenix?
by Yarrow Madrona 21 Apr '14

21 Apr '14

Hello, I recently posted a question about stalled R-factors and and obtained excellent help resulting in the realization that I have tNCS even though it is not picked up by X-triage. I know the transformation matrix of one molecule onto another but I am not sure how to input this into phenix (both the translation and the rotation) to improve refinement. Is there a way to do this? I'm sorry if this has already been covered. -Yarrow

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Re: [phenixbb] Phenix composite omit map
by Chen Zhao 21 Apr '14

21 Apr '14

Dear all, Thank you all for your help and the program is running now. However, I met a AttributeError as " 'twin_model_manager' object has no attribute 'f_model_scaled_with_k1' ". Sorry for so many problems. Thank you so much, Chen On Mon, Apr 21, 2014 at 1:13 PM, Chen Zhao <c.zhao(a)yale.edu> wrote: > Dear Engin, > > Thank you so much for your reply! Yes, this is the problem because I am > using phenix-1.8.4-1496. I will download the newest version! > > Best, > Chen > > > On Mon, Apr 21, 2014 at 1:10 PM, Engin Özkan <eozkan(a)uchicago.edu> wrote: > >> Dear Chen, >> >> What version of Phenix are you using? phenix.composite_omit_map was >> recently added (post 1.8.4 release). Are you using a recent nightly >> (presumably dev-1579 as you suggest or even newer, like the release >> candidate for 1.9)? >> >> Engin >> >> >> On 4/21/14, 12:05 PM, Chen Zhao wrote: >> >> Thank you Tom, >> >> I understand what "command not found" mean, but I already sourced >> "phenix_env" in my bashrc. "phenix.list" works, also I have already run >> "phenix.autosol", "phenix.autobuild", "phenix.refine" without any problems. >> >> Thank you so much again! >> >> Sincerely, >> Chen >> >> >> On Mon, Apr 21, 2014 at 1:01 PM, Terwilliger, Thomas C < >> terwilliger(a)lanl.gov> wrote: >> >>> Hi Chen, >>> >>> "command not found" usually means the shell cannot find a particular >>> command. It often can be fixed by sourcing the right setup commands. >>> >>> If you type: >>> >>> phenix.list >>> >>> does it also say "command not found"? If so, you just need to source >>> the phenix version you want. When you install it phenix lists where this >>> directory is...If you are on a mac you will say something like this: >>> >>> >>> source /Applications/PHENIX-1.8.3-1479/Contents/phenix-1.8.3-1479/phenix_env >>> >>> and you can put that in your .cshrc file too (if you are using csh). >>> >>> Let me know if that doesn't do it! >>> All the best, >>> Tom T >>> >>> >>> >>> >>> On Apr 21, 2014, at 10:53 AM, Chen Zhao wrote: >>> >>> Dear all, >>> >>> Hello! I am now running into a simple technical problem but I just >>> cannot figure it out. I am trying to create a composite omit map by phenix, >>> but when I typed in the command phenix.composite_omit_map XXX.eff based >>> on the instructions on >>> http://www.phenix-online.org/version_docs/dev-1579/composite_omit_map.htm, >>> I got the error message "command not found". Could anybody help me out? >>> >>> Thank you so much in advance! >>> >>> Sincerely, >>> Chen >>> >>> >>> >> >> >> _______________________________________________ >> phenixbb mailing [email protected]://phenix-online.org/mailman/listinfo/phenixbb >> >> >> -- >> Assistant Professor >> Dept of Biochemistry and Molecular Biology >> University of Chicago >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> >

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Berkeley Ligands workshop: registration deadline tomorrow
by Peter Zwart 21 Apr '14

21 Apr '14

Dear All, On May 2, 2014 the BCSB will be hosting a full day event dedicated to ligands in the life sciences. Access is free, but is limited to 30 participants. The lectures will be streamed allowing remote participation to this event. For onsite and remote attendance, please register to receive further instructions. The registration for on-site participation will be on a first come, first serve basis and will close tomorrow at noon. The program will cover structural science associated with ligands in the life sciences. Viewpoints from macromolecular crystallography, quantum chemistry, small molecule crystallography and solution scattering will provide the participants with a 360-degree perspective of the role of and technology associated with ligands in structural biology. Please have a look at https://sites.google.com/a/lbl.gov/ligands/home for more information. Regards Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Research Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org SASTBX: http://sastbx.als.lbl.gov -----------------------------------------------------------------

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Re: [phenixbb] Phenix composite omit map
by Terwilliger, Thomas C 21 Apr '14

21 Apr '14

Hi Chen, "command not found" usually means the shell cannot find a particular command. It often can be fixed by sourcing the right setup commands. If you type: phenix.list does it also say "command not found"? If so, you just need to source the phenix version you want. When you install it phenix lists where this directory is...If you are on a mac you will say something like this: source /Applications/PHENIX-1.8.3-1479/Contents/phenix-1.8.3-1479/phenix_env and you can put that in your .cshrc file too (if you are using csh). Let me know if that doesn't do it! All the best, Tom T On Apr 21, 2014, at 10:53 AM, Chen Zhao wrote: Dear all, Hello! I am now running into a simple technical problem but I just cannot figure it out. I am trying to create a composite omit map by phenix, but when I typed in the command phenix.composite_omit_map XXX.eff based on the instructions on http://www.phenix-online.org/version_docs/dev-1579/composite_omit_map.htm, I got the error message "command not found". Could anybody help me out? Thank you so much in advance! Sincerely, Chen

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Re: [phenixbb] Stalled refinement
by Dale Tronrud 19 Apr '14

19 Apr '14

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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(a)daletronrud.com <mailto:[email protected]>> 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(a)lbl.gov > <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> wrote: > > >> What does triage say about translation NCS? > > >> On Thu, Apr 17, 2014 at 4:25 PM, Yarrow Madrona >> <amadrona(a)uci.edu > <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> 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 >> list phenixbb(a)phenix-online.org >> <mailto:[email protected]> >> <mailto:[email protected] > <mailto:[email protected]>> >> 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(a)lbl.gov > <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> ][ > 1-510-495-2506 <tel:%5B%201-510-495-2506> ] > > > > >> _______________________________________________ phenixbb mailing >> list phenixbb(a)phenix-online.org >> <mailto:[email protected]> >> http://phenix-online.org/mailman/listinfo/phenixbb > > _______________________________________________ phenixbb mailing > list phenixbb(a)phenix-online.org > <mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/phenixbb > > -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (MingW32) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlNSKBMACgkQU5C0gGfAG12g4gCgqgM2umswKaUkxKYQFccDXeOc 3GgAoL5FjHVPUKyK+jkwLQ/BaVv15iiW =Phy4 -----END PGP SIGNATURE-----

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Re: [phenixbb] Stalled refinement
by Kay Diederichs 18 Apr '14

18 Apr '14

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(a)uni-konstanz.de <mailto:[email protected]>> > 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(a)uni-konstanz.__de > <mailto:[email protected]> > <mailto:kay.diederichs@uni-__konstanz.de > <mailto:[email protected]>>> > > 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/Refinem… > <http://strucbio.biologie.uni-__konstanz.de/ccp4wiki/index.__php/Refinement#…> > > > <http://strucbio.biologie.uni-__konstanz.de/ccp4wiki/index.__php/Refinement#… > <http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Refinement#what…>> > > 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(a)phenix-____online.org > <mailto:phenixbb-request@phenix-__online.org> > <mailto:phenixbb-request@__phenix-online.org > <mailto:[email protected]>>: > > > Date: Thu, 17 Apr 2014 16:25:00 -0700 > From: Yarrow Madrona<amadrona(a)uci.edu > <mailto:[email protected]> <mailto:[email protected] > <mailto:[email protected]>>> > To: PHENIX user mailing list<phenixbb(a)phenix-online.____org > <mailto:phenixbb@phenix-__online.org > <mailto:[email protected]>>> > > Subject: [phenixbb] Stalled refinement > Message-ID: > > > <__CAMHjG6bPE4q1xWidpE2VwFMJ9qLS____qjtLRuLMM1ef9vWBHBfZKg(a)mail.____gmail.com > <http://gmail.com> > > <mailto:CAMHjG6bPE4q1xWidpE2Vw__FMJ9qLSqjtLRuLMM1ef9vWBHBfZKg@__mail.gmail.com > <mailto:CAMHjG6bPE4q1xWidpE2VwFMJ9qLSqjtLRuLMM1ef9vWBHBfZKg@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%20c… > <https://www.dropbox.com/s/__2zsajl5o091k50r/CYP142A2-__032814_21_rf%20copy.…> > > > <https://www.dropbox.com/s/__2zsajl5o091k50r/CYP142A2-__032814_21_rf%20copy.… > <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 >

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Re: [phenixbb] Stalled refinement
by Kay Diederichs 18 Apr '14

18 Apr '14

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… 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(a)phenix-online.org: > Date: Thu, 17 Apr 2014 16:25:00 -0700 > From: Yarrow Madrona<amadrona(a)uci.edu> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: [phenixbb] Stalled refinement > Message-ID: > <CAMHjG6bPE4q1xWidpE2VwFMJ9qLSqjtLRuLMM1ef9vWBHBfZKg(a)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 > > 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 >

2 2

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 > ] >

3 4

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

3 2

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

1 0

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

2 1

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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

2 1

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

2 1

PhD position in Structural Biology in Norway
by Hans Petter Hersleth 10 Apr '14

10 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 -----------------------------------------------------------------------------------------------

1 0

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

1 0

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

1 0

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

2 1

fwd: Deadline is approaching: CCP4 crystallographic summer school in USA, at APS, June 24-July 2
by Nathaniel Echols 08 Apr '14

08 Apr '14

---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Date: Tue, 8 Apr 2014 15:46:36 +0000 Subject: Deadline is approaching: CCP4 crystallographic summer school in USA, at APS, June 24-July 2 Dear Colleagues, We would like to remind you that the application deadline for the annual CCP4/APS Crystallographic Summer School in at the end of this week. The original announcement with some useful details is below. With best wishes, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ------------------------------ Dear Colleagues, We are pleased to announce the seventh annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2014/index.php *Title:*"CCP4 crystallographic school: From data collection to structure refinement and beyond" *Dates*: June 24 to July 2. *Site:* Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA *The school content: *Data collection workshop the first two days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three sections - lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. *Applicants*: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. *Application*: Application deadline is April 11. The application form, the program, contact info and other details can be found at http: http://www.ccp4.ac.uk/schools/APS-2014/index.php<http://www.ccp4.ac.uk/schools/APS-2013/index.php> *Fees: *There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers can help make the reservations at economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

1 0

GRC on Diffraction Methods: end July 2014
by Anastassis Perrakis 08 Apr '14

08 Apr '14

Dear all, We are getting closer and closer to the 2014 edition of my favorite Gordon Research Conference (https://www.grc.org/programs.aspx?year=2014&program=diffrac ) on Diffraction Methods in Structural Biology "Faster, Smaller, Better: Novel Technologies for Diffraction Experiments in Molecular Biology and Drug Discovery" , which this year will also feature before it starts the Gordon Research Seminars "Towards Integrative Structural Biology" (https://www.grc.org/programs.aspx?year=2014&program=grs_diff), targeting young scientists! Thanks to INSTRUCT (http://www.structuralbiology.eu) there will be four fellowships for young European researchers coming originally from an INSTRUCT member country or working in an INSTRUCT member country (http://www.structuralbiology.eu/resources/countries). Each fellowship will amount to 750 Euro, covering registration for both the GRC and the GRS, and all local expenses. It is a condition that you have to attend both the GRS and the GRC and submit a poster for both events. If you want to apply for such a fellowship, please send me an email reply (maintain the subject line please), including a single-page PDF file, a very short CV, an equally short abstract of your research, and a motivation statement explaining why you think this event is crucial for your career. Please include the email of your direct supervisor in the end of this letter, and a statement that she/he has agreed to cover the travel expenses for you to attend, if your fellowship application comes through. The deadline for receiving these letters is Wednesday 16 April at 12:CET (yes, thats less than a week from now! get writing!). The letters will be reviewed by an INSTRUCT panel, and the chosen four candidates will get a notification by the 8th of May! And, of course, I do take this opportunity to remind to everyone that the (almost) final program is on-line, we have an absolutely amazing group of speakers lined up, and the available places are filling up fast! So please remember to register on time! Looking forward to see you all at Bates College for what I trust you can make an exciting and memorable meeting! Best regards, Tassos PS If the file is not PDF, if its more than one page, if the characters you use are too small to read, etc etc, don't be too surprised if you do not get the travel fellowship award! Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

1 0

fix part of structure during refinement
by Jorge Iulek 08 Apr '14

08 Apr '14

Dear all, I want to test a refinement in which I fix part of my structure (say, residues 1 to 244 in chains C and D, and chains A and B completely) while the rest is to be refined with annealing. From the manual and http://www.phenix-online.org/pipermail/phenixbb/2009-June/013358.html, I have in my parameter file: " ... refine { strategy = *individual_sites individual_sites_real_space rigid_body \ individual_adp group_adp tls *occupancies group_anomalous sites { individual = ( chain C and resseq 245:259 ) or ( chain D and resseq 245:259 ) torsion_angles = None rigid_body = None } ... " I thought atoms out of the selection in the output structure (chains A and B + residues 1 to 244 in chains C and D) would keep the same coordinates as they were input. But I see all structure atoms changed coordinates. I also tried to turn off tls and ncs usage, but the picture is the same. What do I miss here, to be able to fix some atoms during refinement? Thanks, Jorge

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Tenure track junior Group Leader positions at IEO, Milan, Italy
by Sebastiano Pasqualato 04 Apr '14

04 Apr '14

Dear all, please find enclosed the details to apply for junior Group Leader positions in Experimental and Computation Cancer Biology, open at the European Institute of Oncology, in Milan, Italy. -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEO_XtalUnit -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEO_XtalUnit

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calculating anomalous differences from a model
by Jonathan Grimes 04 Apr '14

04 Apr '14

Given a refined protein structure, is there an straightforward way to calculate the anomalous differences as a function of resolution, at wavelength X. many thanks jon Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer DIAMOND Research Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: Jonathan(a)strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547

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determining molprobity version?
by Pete Meyer 01 Apr '14

01 Apr '14

Hi, I may be missing something obvious, but how do I determine which version of molprobity is being used for generating the clash scores reported by phenix.model_vs_data ? Pete

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error estimates on coordinates
by Benoît Masquida 27 Mar '14

27 Mar '14

Hello, Can someone shed light on the way coordinates errors are obtained in REMARK 3 using maximum of likelihood as compared to Luzzati or sigmaa? What article can be cited in this respect? Thanks in advance. Benoit -- Benoît Masquida Chargé de Recherche CNRS GMGM, UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB, 21, rue René Descartes 67084 Strasbourg b.masquida(a)unistra.fr

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phenix.pdbtools model_statics=true
by Maehigashi, Tatsuya 26 Mar '14

26 Mar '14

Hi all, What would be the best way to define the "selection" to show average B factors using phenix.pdbtools from command line? I've tried several ways using something like... phenix.pdbtools XXXXX.pdb stop_for_unknown=false model_statistics=true selections="chain QA or chain RA" However, the output always contain the standard/default "ADP statistics" table only (not for the selection I specified). Yes, I'm aware of the GUI option (under other tools) and it works great. However, I'm trying to compute average b for 9 coordinates under 4 separate categories (protein, RNA, ligands... and such), and I think it'll be a lot easier from the command line (using some quick script, for example). Any input will be appreciated! "T" ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Obtaining just the Wilson B with Xtriage
by Morten Grøftehauge 26 Mar '14

26 Mar '14

Hi guys, Is there a way to just have phenix.xtriage compute and output the Wilson B factor and not do everything else? I want to run it on a lot of files and that would simplify things. Cheers Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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2014 workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 25 Mar '14

25 Mar '14

Second announcement Fifth Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 16 - June 20, 2014 Application deadline: April 18, 2014 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome. However the course organization may not be able to offer travel or accommodation support. The number of participants will be limited to 15. There is no registration fees for all selected participants. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (for graduate students only; 1/2 to 1 page), should be sent electronically to meilleurf(a)ornl.gov<mailto:[email protected]> before April 18, 2014. Detailed information can be found on the course web page: http://neutrons.ornl.gov/conf/gcnb2014/ Flora Meilleur, Ph. D Assistant Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

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xtriage reindexing suggestions
by Todd Jason Green 24 Mar '14

24 Mar '14

Hello all- I am trying to merge a few partial Se datasets. I am certain that I will have to reindex one or more to make sure that + and - reflections are not jumbled up. Can someone confirm that xtriage take this into account in suggesting to reindex one dataset in relation to a reference dataset? ie. does it use something like maximizing the anomalous signal in suggesting whether or not reindexing is necessary? I think the below suggests as much but I wanted confirmation: Automatic re-indexing For each data set supplied (other than the first data set given), all possible re-indexing matrices are derived as described by Grosse-Kunstleve et al. (2005). Each data set isautomatically re-indexed using the matrix that maximizes the correlation of amplitudes Have a good weekend. -Todd My Example: Reference analyses The following reindexing operators have been found: ------------------------------------------------- | Operator | Correlation | matches (%) | choice | ------------------------------------------------- | -k,h,l | 0.874 | 70.1 | <--- | | h,k,l | 0.032 | 76.7 | | ------------------------------------------------- If the data is reindexed with operator (-k,h,l), the correlation of the intensities to the reference data is maximized. sx205b_anom.sca This can be done for instance with: phenix.reflection_file_converter sx205b_anom.sca --change_of_basis="-k,h,l" <output_options>

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Multiprocessor refine
by Kenneth A. Satyshur 23 Mar '14

23 Mar '14

The FAQ on the web says that phenix.refine uses multiprocessors, yet only phenix.autobuild seems to use MP. Do I need a special version of Phenix? I am using GUI 1.8.4-1496 >How can I use multiple processors to run a job? >Only AutoBuild(http://www.phenix-online.org/documentation/autobuild_gui.htm), LigandFit(http://www.phenix-online.org/documentation/ligandfit_gui.htm), phaser.MRage(http://www.phenix-online.org/documentation/MRage.htm), phenix.refine(http://www.phenix-online.org/documentation/refine_gui.htm), the structure comparison GUI(http://www.phenix-online.org/documentation/structure_comparison.htm), and phenix.find_tls_groups support runtime >configuration of parallel processing. In most cases this is done by adding the "nproc" keyword, for instance: etc RHEL6 x86_64 thanks kas -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207

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Fwd: Reminder: CCP4 crystallographic summer school in USA, at APS, June 24-July 2
by Nathaniel Echols 17 Mar '14

17 Mar '14

---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Cc: Date: Mon, 17 Mar 2014 21:13:27 +0000 Subject: Reminder: CCP4 crystallographic summer school in USA, at APS, June 24-July 2 Dear Colleagues, This is a reminder for approaching deadline to apply for the CCP4 Crystallographic Summer School to be held in June at the APS, near Chicago. Please see the original announcement below for more details. We hope to see you at APS in June. With best wishes, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ------------------------------ Dear Colleagues, We are pleased to announce the seventh annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2014/index.php *Title:*"CCP4 crystallographic school: From data collection to structure refinement and beyond" *Dates*: June 24 to July 2. *Site:* Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA *The school content: *Data collection workshop the first two days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three sections - lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. *Applicants*: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. *Application*: Application deadline is April 11. The application form, the program, contact info and other details can be found at http: http://www.ccp4.ac.uk/schools/APS-2014/index.php<http://www.ccp4.ac.uk/schools/APS-2013/index.php> *Fees: *There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers can help make the reservations at economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov __._,_.___ Reply via web post<https://groups.yahoo.com/group/cnsbb/post;_ylc=X3oDMTJwdmJpN3JlBF9TAzk3MzU5…> Reply to sender <[email protected]?subject=Re%3A%20Reminder%3A%20CCP4%20crystallographic%20summer%20school%20in%20USA%2C%20at%20APS%2C%20June%2024-July%202> Reply to group <[email protected]?subject=Re%3A%20Reminder%3A%20CCP4%20crystallographic%20summer%20school%20in%20USA%2C%20at%20APS%2C%20June%2024-July%202> Start a New Topic<https://groups.yahoo.com/group/cnsbb/post;_ylc=X3oDMTJldnZiMm5wBF9TAzk3MzU5…> Messages in this topic<https://groups.yahoo.com/group/cnsbb/message/2257;_ylc=X3oDMTM0dDhrM2VpBF9T…>(1) -------------------------------------------------------- List information at http://groups.yahoo.com/group/cnsbb. Posting is only allowed for members of this list. Visit Your Group<https://groups.yahoo.com/group/cnsbb;_ylc=X3oDMTJlazc1ZTluBF9TAzk3MzU5NzE0B…> [image: Yahoo! Groups]<https://groups.yahoo.com/;_ylc=X3oDMTJkZGZ1bzZpBF9TAzk3NDc2NTkwBGdycElkAzMw…> * Privacy <https://info.yahoo.com/privacy/us/yahoo/groups/details.html> * Unsubscribe <cnsbb-unsubscribe(a)yahoogroups.com?subject=Unsubscribe> * Terms of Use <https://info.yahoo.com/legal/us/yahoo/utos/terms/> . __,_._,___

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MRage run
by Jobichen Chacko 17 Mar '14

17 Mar '14

Dear All, I am running a molecular replacement using MRage program for almost 1 week with 4 threads, but yet to finish the run. I am using Phenix Version dev-1549 I am having a pretty big protein (around 100 KDa). I gave data file, sequence file, one model pdb and output from HHpred as input. Is there anyway to to find out when it is going to finish the run, or I can extract any information from the current run, if I manually end the run? Thank you. Jobi

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phasing high(er) resolution anomalous difference maps with low resolution phases
by Todd Jason Green 13 Mar '14

13 Mar '14

Hello all- I am working on a huge protein assembly(monomer is ~3000 amino acids, large cell ~200, ~200, ~520) that has between 200 and 300 Se-met residues in the asymmetric unit(depending on the number of molecules I pick in the a.u.). I believe I have low resolution phasing from another heavy atom with limits to ~ 6.2 angstrom. Density modified FOMs dip below 0.6 at that point. I can see many tubes that have the diameter of model alpha helices. I ran phenix.find_helices_strands with the helices_before_trace=True option and got a series of helices encompassing about 3400 residues. Assuming that the phasing on the low resolution derivative is true, is it better to use phasing from the lower resolution derivative or phasing from the helical models to fish out the Se-Met sites via an anomalous difference Fourier? I assume I'm stuck at 6.2 for the derivative phasing though i guess i could extend phasing from the map a little further. How far is too far? How high of resolution can I phase from the helices (or from the derivative map for that matter) and still get accurate enough phasing to yield reliable difference peaks to find the Se sites. I have a couple Se-met datasets between 3 and 2.5 angstroms. What sigma levels should I expect for the difference peaks? also, what is the best way to pick the highest difference peaks in the anomalous difference fourier? I didn't see a tool in phenix. "find difference peaks and holes" seems like a logical choice but it seems to want to structure. I've just created maps and used the very old and reliable peakmax in ccp4. I have solved structures like this before but with a lot more info on ncs, envelopes, ncs averaging and a much much smaller protein. I remember getting sites and plugging them into resolve with scripts where you could fix them/or not and phase without looking for more sites, no build etc. Can i just enter sites and phase followed by density modification with one of the gui programs. any comments would be appreciated? and thanks in advance. -Todd

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Postdoctoral position available
by Peter Zwart 11 Mar '14

11 Mar '14

Dear All, The Berkeley Center for Structural Biology at Lawrence Berkeley National Lab is looking for a postdoctoral fellow to work on the development of computational methods aimed at improving the overall quality of crystallographic data and its resulting atomic models. The results of this work will be integrated into the Berkeley Center for Structural Biology (BCSB) crystallography beam lines at the Advanced Light Source. Please have a look at the job posting and contact me for more information: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=77796 Regards Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Research Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org SASTBX: http://sastbx.als.lbl.gov -----------------------------------------------------------------

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phenix error
by SD Y 04 Mar '14

04 Mar '14

Hi, Could you please tell me why am I getting this error " No atom selected: "name O and chain W and resname HOH and resseq 69". Log file ends as follows: ============================= Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 7 Type Number sf(0) Gaussians Zn2+ 1 27.88 1 S 10 15.96 2 P 2 14.95 2 Mg2+ 3 9.96 1 O 635 7.97 2 N 523 6.97 2 C 1983 5.97 2 sf(0) = scattering factor at diffraction angle 0. ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ======================== Summary of geometry restraints ======================= Number of disulfides: simple=0, symmetry=0 Custom bonds:Sorry------------------------------ Thanks a lotSDY

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