- 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 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

1 0

Phenix validate without map/mtz?
by Oliver Clarke 07 Sep '16

07 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.

3 3

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

2 1

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 30 Aug '16

30 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

1 0

polder map
by Kaziaa 29 Aug '16

29 Aug '16

Dear Phenix users, i am wondering if anyone has used phenix polder in Windows machine. Any kind of help would me appreciated !! Regards Kazi

3 2

Meaning of "resolution" keyword for phenix.real_space_refine with mrc/ccp4 map input?
by Oliver Clarke 28 Aug '16

28 Aug '16

Hi, What exactly does phenix.real_space_refine do with the mandatory "resolution=" keyword when refining a model against a ccp4/mrc formatted map? Is this purely for adjusting restraints etc, or does phenix internally low-pass filter or resample the map based on this parameter? This seems like a basic question, so I apologize if the answer is staring me in the face, but I couldn't see it in the online documentation or in the output of phenix.real_space_refine --help. Cheers Oliver.

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discrepancies between completeness stats
by Kendall Nettles 23 Aug '16

23 Aug '16

Dear PHENIX developers, We are getting a group of structures ready for publication and noticed that the table 1 description of the completeness is showing higher completeness in the last shell than overall. See Table 1, attached, for one example, with completeness at 81.73 (96.75). This table was calculated from the last major release of PHENIX, and was the same on the latest nightly build. The data was highly anisotropic so we truncated it with the UCLA diffraction anisotropy server. Validation program suggests completeness is 13% in highest res shell, which makes more sense with anisotropic data. I also noticed that the refinement log lists the overall completeness at 85% while the validation and table 1 programs give 82%. Thanks for you advice! Kendall

1 0

Merged data for "Table 1"
by Yufan Wu 10 Aug '16

10 Aug '16

Dear all, I am going to generate “Table 1” by Phenix. However, my data.mtz file was merged from 2 HKL file (2 different datasets). What should I input in “unmerged data"? Thank you in advance! Best, Yufan Regards, Yufan Wu The Plueckthun Lab www.bioc.uzh.ch/plueckthun <http://www.bioc.uzh.ch/plueckthun>Phone: +41 44 635 5574

2 1

Mg is driving me crazy
by Almudena Ponce Salvatierra 09 Aug '16

09 Aug '16

Dear all, I am refining a structure that showed two positive peaks larger than 8 sigma. I assigned them as Mg ions, since I have them in the crystallization condition and also because it make sense, according to where they are located. However when I refine there's still all this green blob around the already properly placed Mg ions. I don't know why, they don't show large thermal factors or anything suspicious... I'm refining individual sites, individual adps, and TLS groups. The resolution I am talking about is 2.5 A. Any thoughts on this? Thank you very much Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

3 2

Phenix.refine peptide chain break
by Booe, Jason M (HSC) 29 Jul '16

29 Jul '16

Dear all, I am refining a structure after renumbering my chain such that there is a gap in numbering (i.e. chain A ends at 350 and then starts again at 1000) as this has numbering has been recommended for us to use by the PDB for our fusion proteins. I'm having issues with Phenix.refine not understanding that their is still a peptide bond and breaks the chain and pushes the atoms away. There is no TER card between the chains and I've used LINK records as well to no avail. I'm wondering how to properly deal with this. Thanks, Jason

4 5

Refine pixel size of map (for EM data)?
by Oliver Clarke 26 Jul '16

26 Jul '16

Hello, I wonder whether it would be possible to add an option for phenix.real_space_refine to allow refinement of the pixel size of the map (or the unit cell dimensions - just an overall size scale factor), and write out the altered map at the end of refinement. Although we try to calibrate this as best as we are able at the time of data collection, it is never perfect - for example, in one case I have dealt with, our nominal pixel size out of the scope is 1.19 Å, but the pixel size calibrated based on a crystal structure of a fragment of the protein is 1.25 Å. This is not a huge difference, but it is sufficient I think to have a substantial impact on refinement, particularly as regards clash assessment and H-bond/sec struc restraints. In cases where one does not have a solved crystal structure to use for calibration, perhaps refining the pixel size in conjunction with the geometry might be of some use? Cheers, Oli

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Phenix download issues
by Billy Poon 25 Jul '16

25 Jul '16

Dear all, There is currently an issue with our file server, so Phenix downloads are not unavailable. I will update the list when the website is fully functional. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

1 1

Fall 2016 MicroED workshop at Janelia Research Campus (Reminder)
by Hattne, Johan 21 Jul '16

21 Jul '16

Reminder: the deadline for applications for the Fall 2016 MicroED Workshop is August 1, 2016 (11:59 PM EDT). The original announcement is included below. The second installment of the MicroED workshop will be held at Janelia Research Campus (Ashburn, VA) November 13-16, 2016, hosted by Tamir Gonen. MicroED is a cryo-EM method that uses electron diffraction to facilitate structure determination from sub-micron sized 3D crystals of biological material. MicroED uses equipment and procedures that are standard on many cryo-EM:s, and because of this the technique can be easily adopted in labs and facilities around the world. To encourage the widespread use of MicroED we are offering this workshop to teach microscopists how to perform the technique and adopt it at their own institutions. The first MicroED workshop was held in February of 2016 and was heavily oversubscribed. For this reason we are offering a second workshop. There is no registration fee for participation, and Janelia will provide on-site housing and meals. Attendees are expected to cover their own travel expenses and must be able to stay for the duration. Space in the course is limited. The application deadline is August 1, 2016 (11:59 PM EDT). For more details and to apply, visit https://www.janelia.org/you-janelia/conferences/microed-workshop-1. // Best wishes; Johan, on behalf of the organizers Research Specialist @ Gonen Lab ____________________________________________________ Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

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Berkeley Server Downtime (24 hours, 7/22 - 7/23)
by Billy Poon 20 Jul '16

20 Jul '16

Dear all, On Friday, July 22, our servers will be shut down starting at 5:00 pm Pacific for scheduled maintenance in our building. We expect that the servers will be available the next day (7/23) by 5:00 pm Pacific at the latest. This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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MolProbity C-beta outliers
by Yufan Wu 18 Jul '16

18 Jul '16

Dear all, Anyone knows the definition of “angle” shown in the report of "MolProbity C-beta position outliers” after refinement ? It means the bond angle or dihedral angle? Between which atoms or planers? I am just wondering the definition of it. Thank you in advance! Best, Yufan Wu Regards, Yufan Wu The Plueckthun Lab www.bioc.uzh.ch/plueckthun <http://www.bioc.uzh.ch/plueckthun>Phone: +41 44 635 5574

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MolProbity C-beta outliers
by Yufan Wu 15 Jul '16

15 Jul '16

Dear all, Anyone knows the definition of angle in "MolProbity C-beta position outliers”? See the screenshot below. It means the bond angle or dihedral angle? Between which atoms or planers? I am just wondering the definition of it. Thank you in advance! Best, Yufan Wu Regards, Yufan Wu The Plueckthun Lab www.bioc.uzh.ch/plueckthun <http://www.bioc.uzh.ch/plueckthun>Phone: +41 44 635 5574

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Amber in phenix
by R. Gasper-Schönenbrücher 12 Jul '16

12 Jul '16

Hi all, I am trying to run amber from phenix with a standard pdb file, no co-factors etc and struggle already at the phenix.AmberPrep script. For unknown reasons, the .prmtop file stays empty (0 bytes). I have tried to figure out from the amber python scripts, where the problem might be, but didn't find anything obvious (the "self.ns_names" variable stays empty) The leap log files states two problems: 1) ......Nonterminal, was not found in name map. (for every single amino acid) 2) FATAL: Atom .R<MET 1>.A<N 1> does not have a type. (for every single atom) which ends up in: "Failed to generate parameters Parameter file was not saved." There is no .map2 file generated. Phenix version: dev-2463 Amber: Ambertools 16 Every help is highly appreciated. Many thanks! Best, Raphael -- Raphael Gasper-Schönenbrücher Universität Bochum AG Proteinkristallographie, Lehrstuhl für Biophysik, NDEF 04/316 Universitätsstraße 150 44801 Bochum Germany Tel: +49 (0)234-32 27086 Fax: +49 (0)234-32 14762

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How to assign Half occupancy to metal ion in protein crystal
by Sharan Karade 08 Jul '16

08 Jul '16

Dear all, I am refining the protein structure and i want add metal ion in the structure, the site is present in between protein chain and its symmetry mate. when i added metal and refined, it was showing the high B factor and symmetry related metal on the same site. i want to assign the occupancy half and refine but in coot i am unable to do. Is there any method to do this. Thanks in Advance -- Sharan C/O Dr. J V Pratap Senior Research Fellow, CSIR-Central Drug Research Institute, Lucknow

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Question about restrain of a nonstandard peptide
by Yufan Wu 06 Jul '16

06 Jul '16

Dear Phenix Developers/Users, I have a question regarding how to generate a correct restrain for a whole nonstandard peptide and how do run refinement correctly. The nonstandard peptide in my structure is pepstatin A (IVA Val Val STA Ala STA). I manually put the pepstatin A in the density and generated the cif files for IVA and STA and run the refinement with them. After refinement, the whole pepstatin A explored as pieces, which I guess the program treated the pepstatin A as single amino acids. By the way, I also manual input the “LINK” information in the input pdb file as below, LINK C VAL L 3 N STA L 4 1555 1555 LINK N ALA L 5 C STA L 4 1555 1555 LINK C ALA L 5 N STA L 6 1555 1555 And also, when I use the “Real Space Refine Zone” by clicking two atoms for the whole pepstatin A in coot, it exploded again, although I input the same cif file in coot as well. The data quality is not good (2.9 A with CC1/2=12), thus it is difficult to place amino acid individually to fit the destiny. In the PDB, there are several structures containing the pepstatin A, such as 4TVG, 4AUC. They have the pepatatin A sequence as VVVXAX, but none of them lists the constrains. Would you please help me and let me know how can I continue with refinement? Please let me know if you need more information. Thank you vey much! Yufan Wu Regards, Yufan Wu The Plueckthun Lab www.bioc.uzh.ch/plueckthun <http://www.bioc.uzh.ch/plueckthun>Phone: +41 44 635 5574

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