- phenixbb - phenix-online.org

Partial Model for Mol Rep.
by Yuri 03 May '14

03 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 30 Apr '14

30 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 28 Apr '14

28 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 27 Apr '14

27 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 25 Apr '14

25 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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