- phenixbb - phenix-online.org

Option to select array from mtz in phenix.real_space_refine?
by Oliver Clarke 06 Oct '16

06 Oct '16

Hi, I find phenix.real_space refine very effective for initial refinement of a model against a density modified map after molecular replacement (with morphing and reference restraints etc enabled). However, when I do this it seems like if there is more than one array of map coefficients in the file there is no way to select which columns to use, unlike for phenix.refine - would it be possible to add such an option? Currently I just use cad in ccp4 to make a file with the desired columns, but it would be a smoother process if the desired column labels could be specified directly at run time. Cheers Oli

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Highly anisotropic data
by Kogan, Konstantin 06 Oct '16

06 Oct '16

Dear all, I have highly anisotropic data. I was able to solve the structure by MR, and refine it with phenix.refine to Rwork/Rfree=0.28/0.31 with Resolution cutoff 2.64Å and mean B values 114, which is pretty high for such resolution. Though the overall structure makes sense, the maps are quite featureless, no water molecules, and side-chains refinement is a problem. I have tested how the data is anisotropic with Diffraction Anisotropy Server <https://services.mbi.ucla.edu/anisoscale/> (see attached image), which shows clearly, that we don't really have data to 2.64Å in all directions. Though, there are other servers/programs that can deal specifically with anisotropic data e.g. STARANISO anisotropy server <http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi> and then refine with BUSTER, I would like to know if it's possible still to use Phenix with some more advance parameters to actually address the issue of anisotropy and to get maximum out of the data. The space group is P61 2 2, cell parameters are 73, 73, 453, 90, 90, 120 and I have high multiplicity data, but no NCS. Thanks in advance for any input, Kostya -- Konstantin (Kostya) Kogan Postdoctoral researcher Pekka Lappalainen's Lab Institute of Biotechnology University of Helsinki Helsinki, Finland Mobile: +358-(0)45-8994342

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Planarity restraint ignored when dist_esd equal to 0
by Keitaro Yamashita 28 Sep '16

28 Sep '16

Dear PHENIX developers, My colleague noticed that planarity restraint of a ligand was ignored when a cif file in CCP4 monomer library was given to phenix.refine. The cif file was $CLIBD_MON/3/3PG.cif. This was because phenix (mmtbx) ignores planarity restraint when dist_esd is 0. In the line 2055 of mmtbx/monomer_library/pdb_interpretation.py (phenix-1.10.1), plane_atom is not added to the list when (plane_atom.dist_esd in [None, 0]) is True. _chem_comp_plane_atom.dist_esd in 3PG.cif (ccp4-7.0) is all zero except the first atom in the plane definition. As far as I checked, there is no cif file where dist_esd of the first atom of plane is zero. At least, it would be helpful if phenix shows warning in this case. Best regards, Keitaro

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How to define Fobs labels for phenix.refine in command line mode
by Karthikeyan Subramanian 27 Sep '16

27 Sep '16

Dear All, Is it possible to define the Fobs (or) Iobs labels for phenix.refine in command line mode? Thanks Karthikeyan S. IMTECH, Chandigarh India

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Rotamers of unnatural halogenated amino acids
by ancacarl 26 Sep '16

26 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 26 Sep '16

26 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 12 Sep '16

12 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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