- phenixbb - phenix-online.org

Rotamers of unnatural halogenated amino acids
by ancacarl 27 Sep '16

27 Sep '16

Hi, I'm working on the refinement of a protein mutated with an unnatural amino acid that contains one bromine atom. This particular amino acid is present as two rotamers. I've managed to introduce and do refinements with these two unnatural, brominated rotamers in Phenix, but the problem is that when shooting the protein with X-rays about 30-40% of the bromine atoms get knocked off. This means that the sum of the occupancies for the bromine atoms of the rotamers needs to be less than 1.00. However, the total occupancy of all the other rotamer atom pairs must be 1.00. Is there a way in Phenix to refine rotamers of brominated, unnatural amino acids, and at the same time have the total occupancy less than 1.00 for the Br atoms only? Any advice how to solve this is welcome.

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phenix.real_space_refine - mmcif output?
by Oliver Clarke 27 Sep '16

27 Sep '16

Any chance of getting mmcif output in phenix.real_space_refine? Or does it exist and I have just overlooked the option? Right now I can use mmcif as input, but the refined coordinates are still written as pdb (hybrid32). The PDB unfortunately doesn’t accept hybrid32, so I always need to convert to mmcif with phenix.pdbtools prior to deposition - no big deal but would make life easier for large-ish structures. Cheers Oli.

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Registration open: Future of Fragments symposium - Diamond, 28/29 Nov 2016
by Frank von Delft 23 Sep '16

23 Sep '16

Dear all Registration is now open for the Future of Fragments symposium on 28/29 November at Diamond Light Source, UK. http://www.diamond.ac.uk/Home/Events/2016/Future-of-Fragments-Symposium.html Places will be tight, so register early to give us time to gauge whether we must adapt plans. _Overview_ Crystal-based fragment screening of novel protein targets linked to disease has truly come of age: Diamond's XChem facility has been operating a regular user program since 2015, with other synchrotrons soon to follow suit. A progression of user projects have confirmed the power of this approach to discover both diverse chemotypes and unexpected mechanisms of action, especially allosteric binders. At the same time, the continued success in unearthing a rich array of fragment hits has now decisively shifted the bottleneck onto the question of how to translate hits into high potency leads. This challenge has highlighted the need for efficient and scalable methodologies in the areas of library design, label-free assays, computational compound design and the synthesis of complex lead molecules. This symposium aims to highlight the opportunities that must be explored if routine fragment screening is to turn into routine lead discovery. The event will bring together speakers from diverse disciplines to help define the methodology, focus and goals for fragment screening in the coming years. The four sessions will cover: screening methodology; computational methods; new synthetic methods; and automated chemistry.

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Weighting in phenix.real_space_refine
by Oliver Clarke 13 Sep '16

13 Sep '16

Hi all, How does phenix.real_space_refine deal with restraint weighting? Looking at the output of the program, I get the impression that it splits the model up into different chunks, and alters weights locally based on some model/map correlation metric - is this the case (and are there more specific details available), or how does it work otherwise? Cheers, Oliver.

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rosetta installation
by Sebastiano Pasqualato 13 Sep '16

13 Sep '16

Hi there, I am trying to run Phenix Rosetta Refinement on my laptop, which is running MacOSX 10.11.6 (El Capitan) with XQuartz 2.7.9. I have followed the instructions on this page: https://www.phenix-online.org/documentation/reference/rosetta_refine.html <https://www.phenix-online.org/documentation/reference/rosetta_refine.html> and specifically Once you have both a Phenix installation and a Rosetta source distribution, you can build the hybrid system with this command (located in the Phenix tree): rosetta.build_phenix_interface nproc=X Unfortunately, when I do that, the building does not proceed flawlessly, but instead stops with the message the I report below. Has someone gone through the same and can tell me how to set up Rosetta to be used with Phenix? Thanks in advance for the help, Sebastiano Seba@host028:~> rosetta.build_phenix_interface nproc=8 False scons: Reading SConscript files ... xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun Running versioning script ... xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun Done. (0.0 seconds) Number of option files updated: 0 Total 3741 options. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed scons: done reading SConscript files. scons: Building targets ... clang++ -o build/src/release/macos/15.6/64/x86/clang/python/apps/public/AbinitioRelax.o -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/apps/public/AbinitioRelax.cc xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun clang++ -o build/src/release/macos/15.6/64/x86/clang/python/devel/init.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/devel/init.cc xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun clang++ -o build/src/release/macos/15.6/64/x86/clang/python/devel/svn_version.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/devel/svn_version.cc xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun clang++ -o build/src/release/macos/15.6/64/x86/clang/python/protocols/init/init.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/init/init.cc xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun clang++ -o build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/DownstreamRMSEvaluator.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/match/output/DownstreamRMSEvaluator.cc xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun clang++ -o build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/LimitHitsPerRotamerFilter.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/match/output/LimitHitsPerRotamerFilter.cc xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun clang++ -o build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/MatchConsolidator.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/match/output/MatchConsolidator.cc xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun scons: *** [build/src/release/macos/15.6/64/x86/clang/python/apps/public/AbinitioRelax.o] Error 1 clang++ -o build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/MatchEvaluator.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/match/output/MatchEvaluator.cc <http://matchevaluator.cc/> scons: *** [build/src/release/macos/15.6/64/x86/clang/python/devel/init.os] Error 1 scons: *** [build/src/release/macos/15.6/64/x86/clang/python/devel/svn_version.os] Error 1 scons: *** [build/src/release/macos/15.6/64/x86/clang/python/protocols/init/init.os] Error 1 scons: *** [build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/DownstreamRMSEvaluator.os] Error 1 scons: *** [build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/LimitHitsPerRotamerFilter.os] Error 1 scons: *** [build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/MatchConsolidator.os] Error 1 xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun scons: *** [build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/MatchEvaluator.os] Error 1 scons: building terminated because of errors. Seba@host028:~> -- 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/IEOXtalUnit

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To count crystal contacts along a, b or c?
by vincent Chaptal 08 Sep '16

08 Sep '16

Dear community, I would like to count crystal contacts bewteen ASU and symmetrics along the cell axis (a, b, c). Could someone point to me a way to do this? Thank you very much in advance. vincent -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr

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Phenix validate without map/mtz?
by Oliver Clarke 08 Sep '16

08 Sep '16

Hi, Would it be possible to allow for running phenix validate without a map/mtz? I dont always want the RSCC information, and it would be useful to be able to get the geometry stats and sequence check without loading a map (which in the case of EM maps can be very large and will presumably slow things down a lot). Cheers, Oliver.

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Data processing
by Sharan Karade 07 Sep '16

07 Sep '16

Dear All, i had collected the data set on the Bruker X-ray machine (home source), it has its in built data processing software, but i want to process it on HKL2000, but the file format is .srfm and it is not read by HKL2000 soft. in our lab we have. So, i tried to change the detector type, then i came to know that we don't have license to bruker detector, So anyone know how to convert these file into .mccd or.mar, so i can process them. Thank you -- Sharan C/O Dr. J V Pratap Senior Research Fellow, CSIR-Central Drug Research Institute, Lucknow

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Post-doctoral position in membrane protein structure and function, University of Oxford, UK
by Maike Bublitz 06 Sep '16

06 Sep '16

Dear all, a post-doctoral position is available in the research group of Associate Prof. Maike Bublitz at the Department of Biochemistry, University of Oxford. The project aims to understand the structure and function of microbial membrane transport proteins identified as potential new drug targets, using a combination of state-of-the-art structural (X-ray crystallography, cryo-EM) and biochemical/biophysical techniques. Applicants should hold a PhD in a relevant subject area, such as membrane protein biochemistry or structural biology. Experience in native or recombinant membrane protein expression, purification and either structural determination or functional analysis using biochemical and biophysical techniques is essential. Ability to work in a team as well as contribute to supervision activities and excellent verbal and written communication skills are expected. Experience in protein X-ray crystallography and/or cryo-EM is an advantage. To apply for this role and for further details, including the job description and selection criteria, please click on the link below: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_details_form.j… Applications for this vacancy are to be made online by 14th September 2016. PLEASE NOTE: THIS IS A READVERTISEMENT, PREVIOUS APPLICANTS NEED NOT APPLY. Best regards, Maike ************************************************* Dr. Maike Bublitz Associate Professor of Microbial Biophysics Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU United Kingdom phone: +44 (0)1865 613221 maike.bublitz(at)bioch.ox.ac.uk<http://bioch.ox.ac.uk> ************************************************* Dr. Maike Bublitz Associate Professor of Microbial Biophysics Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU United Kingdom phone: +44 (0)1865 613221 maike.bublitz(at)bioch.ox.ac.uk<http://bioch.ox.ac.uk>

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Computational Crystallography Newsletter, Volume 7, Number 2
by Nigel Moriarty 31 Aug '16

31 Aug '16

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. July 2016 <http://www.phenix-online.org/newsletter/CCN_2016_07.pdf> Articles - Working with EIGER data <http://www.phenix-online.org/newsletter/CCN_2016_07.pdf#page=11> - Processing XFEL data with cctbx.xfel and DIALS <http://www.phenix-online.org/newsletter/CCN_2016_07.pdf#page=18> Short Communications - Using Molecular Dynamics Simulations to Enrich the Water Structure in Biomolecular Crystals <http://www.phenix-online.org/newsletter/CCN_2016_07.pdf#page=7> Fitting tips #12 – Twist Tells: better β strands at >3.5Å in x-ray or cryoEM <http://www.phenix-online.org/newsletter/CCN_2016_07.pdf#page=2> Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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