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Abstract deadline is TOMORROW for Diffraction Methods in Structural Biology GRS
by Pearce, N.M. (Nick) 27 Apr '18

27 Apr '18

Dear BB, Tomorrow is the abstract deadline for the Gordon Research Seminar in Diffraction Methods 2018 at Bates College, Maine (28-29th July 2018). Applications/abstracts received after this date (28th April) will still be able to attend and present posters, but will not be considered for oral presentations. This year’s title is Crystallography 2.0: Restructuring the Field Around a New Wave of Experiments We want to have as many young scientists (Post-docs, PhD candidates & Master’s students) at the GRS (and associated GRC) as possible. For Jessica and myself, the 2016 Diffraction Methods GRS & GRC was the best conference we’ve attended during our PhDs, since it allowed us to present our research directly to our peers in a relaxed setting; it also gave many of us the opportunity to gain first-hand experience as session chairs -- an opportunity that is difficult to find as a young scientist. On top of this, the intimate nature and relatively small size of Gordon conferences helped us to build more long-lasting international connections than at any other conference we have attended. Of course, the GRS can only be truly successful if a wide variety of viewpoints are represented — so please consider attending. We would greatly appreciate it if you could also forward this invitation to any young scientists for whom you think this conference might be valuable. You can apply for the seminar (GRS) here: https://www.grc.org/diffraction-methods-in-structural-biology-grs-conferenc…. On this page you can also find a link to the associated Gordon Research Conference (GRC). We hope to see you in July, Nicholas Pearce & Jessica Besaw Chair & Co-Chair, Gordon Research Seminar in Diffraction Methods, 2018

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11th CCP4/APS Crystallographic School in the US
by Qingping Xu 26 Apr '18

26 Apr '18

Just a friendly reminder that the deadline for applying the upcoming CCP4 school at APS is next Wednesday (5/2/2018), please apply or finish your application (if you have already applied) if you wish to participate in the school. Please let us know if you have any questions/concerns. Qingping Xu GMCA/APS Argonne National Laboratory =========== Dear Colleagues, We are pleased to announce the *11th annual CCP4 crystallographic school *“From data collection to structure refinement and beyond” will be held on June 18-25, 2018 at Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at http://www.ccp4.ac.uk/schools/APS-2018/index.php. *Dates*: June 18 through 25, 2018 *Location*: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises two parts: *data collection workshop* and *crystallographic computing workshop*. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). *Applicants*: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. *Application*: Application deadline is *Wednesday May 2nd, 2018*. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2018/index.php *Registration fees*: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals). We hope to see you at the school. Charles, Garib and Qingping

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BCA/CCP4 Summer School in Protein Crystallography at Diamond
by Airlie McCoy 23 Apr '18

23 Apr '18

Applications are now open for the BCA/CCP4 Summer School in Protein Crystallography to be held at Diamond (UK) from Monday 27th August to Saturday 1st September 2018. Note that applications close 18TH MAY 2018 The BCA/CCP4 Protein Crystallography Summer School is intended for students and researchers new to crystallography. Its dual aims are to provide comprehensive training in crystallography and to promote best practise within the British crystallographic community. The lectures cover the gamut of techniques required for a structure solution, from protein expression through to structure validation. Intensively supervised computer tutorials enable students to relate the theory presented in the lectures to practice. Although CCP4 programs will primarily be used in these tutorials, the aim will be to approach crystallographic questions in a software-agnostic manner. There will also be a crystal manipulation and cooling workshop. Note that the course is scheduled during Diamond synchrotron downtime, so there will not be active data collection at the Diamond beamlines. Up to 10 places for those with BBSRC studentships will be fully funded. We recognise that the social programme plays a role in enabling students to make links that may be maintained throughout a research career. There will be a conference dinner, and a number of other events, including a trip to Oxford. For more information see http://www.diamond.ac.uk/Home/Events/2018/BCA-Summer-School.html Application form: https://extranet2.diamond.ac.uk/ISV/BCA/ApplicationForm.aspx

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Abstract deadline is 28th April for Diffraction Methods in Structural Biology GRS
by Pearce, N.M. (Nick) 23 Apr '18

23 Apr '18

Dear BB, There are five more days until the abstract deadline for the Gordon Research Seminar in Diffraction Methods 2018 at Bates College, Maine (28-29th July 2018). Applications/abstracts received after this date (28th April) will still be able to attend and present posters, but will not be considered for oral presentations. This year’s title is Crystallography 2.0: Restructuring the Field Around a New Wave of Experiments We want to have as many young scientists (Post-docs, PhD candidates & Master’s students) at the GRS (and associated GRC) as possible. For Jessica and myself, the 2016 Diffraction Methods GRS & GRC was the best conference we’ve attended during our PhDs, since it allowed us to present our research directly to our peers in a relaxed setting; it also gave many of us the opportunity to gain first-hand experience as session chairs -- an opportunity that is difficult to find as a young scientist. On top of this, the intimate nature and relatively small size of Gordon conferences helped us to build more long-lasting international connections than at any other conference we have attended. Of course, the GRS can only be truly successful if a wide variety of viewpoints are represented — so please consider attending. We would greatly appreciate it if you could also forward this invitation to any young scientists for whom you think this conference might be valuable. You can apply for the seminar (GRS) here: https://www.grc.org/diffraction-methods-in-structural-biology-grs-conferenc…. On this page you can also find a link to the associated Gordon Research Conference (GRC). We hope to see you in July, Nicholas Pearce & Jessica Besaw Chair & Co-Chair, Gordon Research Seminar in Diffraction Methods, 2018

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mtriage error
by Sara Weaver 20 Apr '18

20 Apr '18

Hi all, I'm trying to process some cryoEM data that goes to 2.9 angstroms in phenix. I can't seem to run mtriage on several different builds. Any ideas? I've put the errors below. I've tried making my input map a .mrc, or a .ccp4 and get the same errors. Thanks! Sara [sjweaver@brmaster job099]$ /hotdata/sbgrid/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/build/bin/phenix.mtriage map_file_name=run_class001.mrc ------------------------------------------------------------------------------- phenix.mtriage: Given map file and optionally model and half-map files compute map statistics. How to run: phenix.mtriage model_file_name=m.pdb map_file_name=m.map half_map_file_name_1=m1.map half_map_file_name_2=m2.map Optional: model_file_name=, half_map_file_name_1=, half_map_file_name_2= Feedback: PAfonine(a)lbl.gov phenixbb(a)phenix-online.org ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Input model: ************ No model specified. ------------------------------------------------------------------------------- Box (unit cell) info: ********************* Unit cell: (255.948, 255.948, 255.948, 90, 90, 90) Space group: P 1 (No. 1) Traceback (most recent call last): File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py", line 277, in <module> run(args=sys.argv[1:]) File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py", line 190, in run task_obj.run() File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/modules/cctbx_project/mmtbx/maps/mtriage.py", line 174, in run self._shift_origin() File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/modules/cctbx_project/mmtbx/maps/mtriage.py", line 204, in _shift_origin crystal_symmetry = self.crystal_symmetry) File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/modules/cctbx_project/cctbx/maptbx/__init__.py", line 112, in shift_origin_if_needed assert [sites_cart, crystal_symmetry].count(None) in [0, 2] AssertionError [sjweaver@brmaster job099]$ /hotdata/sbgrid/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/build/bin/phenix.mtriage map_file_name=run_class001.mrc ------------------------------------------------------------------------------- phenix.mtriage: Given map file and optionally model and half-map files compute map statistics. How to run: phenix.mtriage model_file_name=m.pdb map_file_name=m.map half_map_file_name_1=m1.map half_map_file_name_2=m2.map Optional: model_file_name=, half_map_file_name_1=, half_map_file_name_2= Feedback: PAfonine(a)lbl.gov phenixbb(a)phenix-online.org ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Input model: ************ No model specified. ------------------------------------------------------------------------------- Box (unit cell) info: ********************* Unit cell: (255.948, 255.948, 255.948, 90, 90, 90) Space group: P 1 (No. 1) Traceback (most recent call last): File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py", line 287, in <module> run(args=sys.argv[1:]) File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py", line 195, in run task_obj.run() File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/modules/cctbx_project/mmtbx/maps/mtriage.py", line 204, in run self.call(func=self._compute_d_model_b0, prefix="Compute d_model_b0") File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/modules/cctbx_project/mmtbx/maps/mtriage.py", line 185, in call func() File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/modules/cctbx_project/mmtbx/maps/mtriage.py", line 295, in _compute_d_model_b0 map_data = self.box.map_data, AttributeError: 'NoneType' object has no attribute 'map_data' [sjweaver@brmaster job099]$ /hotdata/sbgrid/programs/x86_64-linux/phenix/dev-3063/phenix-dev-3063/build/bin/phenix.mtriage map_file_name=run_class001.mrc ------------------------------------------------------------------------------- phenix.mtriage: Given map file and optionally model and half-map files compute map statistics. How to run: phenix.mtriage model_file_name=m.pdb map_file_name=m.map half_map_file_name_1=m1.map half_map_file_name_2=m2.map Optional: model_file_name=, half_map_file_name_1=, half_map_file_name_2= Feedback: PAfonine(a)lbl.gov phenixbb(a)phenix-online.org ------------------------------------------------------------------------------- Traceback (most recent call last): File "/hotdata/sbgrid/programs/x86_64-linux/phenix/dev-3063/phenix-dev-3063/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py", line 274, in <module> run(args=sys.argv[1:]) File "/hotdata/sbgrid/programs/x86_64-linux/phenix/dev-3063/phenix-dev-3063/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py", line 158, in run params = inputs.params) File "/hotdata/sbgrid/programs/x86_64-linux/phenix/dev-3063/phenix-dev-3063/modules/cctbx_project/mmtbx/maps/mtriage.py", line 130, in __init__ box = self.params.use_box) File "/hotdata/sbgrid/programs/x86_64-linux/phenix/dev-3063/phenix-dev-3063/modules/cctbx_project/iotbx/map_and_model.py", line 115, in __init__ crystal_symmetry = self._model.crystal_symmetry()) AttributeError: 'NoneType' object has no attribute 'crystal_symmetry' ariel:20180417_lookingatRefinej348_focused sjweaver$ /Applications/phenix-dev-3112/build/bin/phenix.mtriage map_file_name=run_ct8_class001.mrc ------------------------------------------------------------------------------- phenix.mtriage: Given map file and optionally model and half-map files compute map statistics. How to run: phenix.mtriage model_file_name=m.pdb map_file_name=m.map half_map_file_name_1=m1.map half_map_file_name_2=m2.map Optional: model_file_name=, half_map_file_name_1=, half_map_file_name_2= Feedback: PAfonine(a)lbl.gov phenixbb(a)phenix-online.org ------------------------------------------------------------------------------- Traceback (most recent call last): File "/Applications/phenix-dev-3112/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py", line 339, in <module> run(args=sys.argv[1:]) File "/Applications/phenix-dev-3112/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py", line 204, in run inputs.model.setup_scattering_dictionaries( AttributeError: 'NoneType' object has no attribute 'setup_scattering_dictionaries' -- Sara J. Weaver *Doctoral Candidate, Jensen Lab* *California Institute of Technology*

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Protein structures sought for CASP13
by Paul Adams 20 Apr '18

20 Apr '18

Posted on behalf of the CASP organizing Committee: Critical Assessment of Techniques for Protein Structure Prediction (CASP) community experiments aim to advance the state of the art in protein structure modeling. Every other year since 1994, CASP collects information on soon-to-be released experimental structures, passes on sequence data to the structure modeling community, and collects blind predictions of structure for assessment. About 100 modeling groups from around the world participate. Results of CASP experiments are published in special issues of the journal PROTEINS (e.g., CASP12: https://onlinelibrary.wiley.com/toc/10970134/86/S1). The success of CASP depends on the generosity of the structure determination community. We are now requesting targets for CASP13 experiment, which will launch at the beginning of May. The CASP community needs modeling targets over a wide range of difficulty, for modeling with and without the aid of templates. X-ray, NMR and cryo-EM structures are welcome. We are particularly interested in membrane proteins, protein complexes, and cryo-EM structures. We are also extending CASP to include more modeling assisted by sparse experimental data, in collaboration with experimental groups in NMR, SAXS, SANS, crosslinking, and FRET. For that, protein material is needed (of course this is not expected for most targets, but if available, it would be much appreciated!). So, if you have anything suitable, we encourage you to mark your PDB deposition as a "CASP target" in the PDB's submission system. Alternatively, you can suggest your protein to CASP directly through the CASP13 target entry page: http://www.predictioncenter.org/casp13/targets_submission.cgi. For those of you who have not provided targets to CASP before, the procedure is simple and fast. We don’t need the structure in advance of its release by the PDB, and if we are notified early enough (a minimum of three weeks before release, more is better) there need be no delay in structure release. More details are available on the web site. CASP target providers are regularly invited to contribute to special issue papers, for example: 2018: Kryshtafovych A, Albrecht R, Baslé A, Bule P, Caputo AT, Carvalho AL, Chao KL, Diskin R, Fidelis K, Fontes CMGA, Fredslund F, Gilbert HJ, Goulding CW, Hartmann MD, Hayes CS, Herzberg O, Hill JC, Joachimiak A, Kohring GW, Koning RI, Lo Leggio L, Mangiagalli M, Michalska K, Moult J, Najmudin S, Nardini M, Nardone V, Ndeh D, Nguyen TH, Pintacuda G, Postel S, van Raaij MJ, Roversi P, Shimon A, Singh AK, Sundberg EJ, Tars K, Zitzmann N, Schwede T. (2018). Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). Proteins 86 (S1), 27-50. doi: 10.1002/prot.25392. PMID: 28960539 2016:  Kryshtafovych A, Moult J, Baslé A, Burgin A, Craig TK, Edwards RA, Fass D, Hartmann MD, Korycinski M, Lewis RJ, Lorimer D, Lupas AN, Newman J, Peat TS, Piepenbrink KH, Prahlad J, van Raaij MJ, Rohwer F, Segall AM, Seguritan V, Sundberg EJ, Singh AK, Wilson MA, Schwede T. (2016). Some of the most interesting CASP11 targets through the eyes of their authors. Proteins 84 (S1), 34-50. doi: 10.1002/prot.24942. PMID: 26473983   2014: Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C, Herzberg O, Lorimer D, Luecke H, Ma X, Nelson DC, van Raaij MJ, Rohwer F, Segall A, Seguritan V, Zeth K, Schwede T. (2014). Challenging the state-of-the-art in protein structure prediction: Highlights of experimental target structures for the 10th critical assessment of techniques for protein structure prediction experiment CASP10. Proteins 82 (S2), 26-42. doi: 10.1002/prot.24489. PMID: 24318984 2011: Kryshtafovych A, Moult J, Bartual SG, Bazan JF, Berman H, Casteel DE, Christodoulou E, Everett JK, Hausmann J, Heidebrecht T, Hills T, Hui R, Hunt JF, Seetharaman J, Joachimiak A, Kennedy MA, Kim C, Lingel A, Michalska K, Montelione GT, Otero JM, Perrakis A, Pizarro JC, van Raaij MJ, Ramelot TA, Rousseau F, Tong L, Wernimont AK, Young J, Schwede T. (2011). Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. Proteins 79 (S10), 6-20. doi: 10.1002/prot.23196. PMID: 22020785 Thanks, CASP organizing committee: John Moult, University of Maryland, USA Krzysztof Fidelis, University of California, Davis, USA Andriy Kryshtafovych, University of California, Davis, USA Torsten Schwede, University of Basel, Switzerland Get in touch: casp(a)predictioncenter.org More information: http://www.predictioncenter.org/casp13/index.cgi Submit a target: http://www.predictioncenter.org/casp13/targets_submission.cgi -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Deadline for the EM and the X-ray bundles of iNEXT extended to 24 April (midnight)
by a.perrakis＠nki.nl 19 Apr '18

19 Apr '18

Dear all, The deadline for the EM and the X-ray bundles of iNEXT is now extended until 24 April (midnight, for all timezones …). For more information http://www.inext-eu.org/inext-em-and-x-ray-bundles/ and to submit a proposal https://www.structuralbiology.eu/submit-proposal/?t=inext Best regards, the INEXT team

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Call for not-yet-released structures as candidates for protein structure predictors
by Susan Tsutakawa 17 Apr '18

17 Apr '18

Critical Assessment of Techniques for Protein Structure Prediction (CASP) community experiments aim to advance the state of the art in protein structure modeling. Every other year since 1994, CASP collects information on soon-to-be released experimental structures, passes on sequence data to the structure modeling community, and collects blind predictions of structure for assessment. About 100 modeling groups from around the world participate. Results of CASP experiments are published in special issues of the journal PROTEINS (e.g., CASP12: Proteins Vol 86, Issue S1, March 2018). The thirteenth CASP round is scheduled to start on May 1, 2018. The organizing committee is particularly keen to include many cryo-EM-derived structure targets in this round. The success of CASP depends on the generosity of the structure determination community. Modeling targets are needed over a wide range of difficulty, for modeling both with and without the aid of templates. Targets that can be modeled based on structural templates should ideally have 50% or less sequence identity to the templates. Access to the structure in advance of its release by the PDB or its publication is not needed. With sufficient notification to CASP (a minimum of three weeks before release, more is better) there is no need to delay structure release. If you have recently determined a novel protein structure and will be depositing it to PDB, please suggest it as a target for CASP by visiting www.predictioncenter.org/casp13/targets_submission.cgi. If you have any questions please contact [log in to unmask] CASP target providers are regularly invited to contribute to special issue papers, for example: 2018: Kryshtafovych A, Albrecht R, Baslé A, Bule P, Caputo AT, Carvalho AL, Chao KL, Diskin R, Fidelis K, Fontes CMGA, Fredslund F, Gilbert HJ, Goulding CW, Hartmann MD, Hayes CS, Herzberg O, Hill JC, Joachimiak A, Kohring GW, Koning RI, Lo Leggio L, Mangiagalli M, Michalska K, Moult J, Najmudin S, Nardini M, Nardone V, Ndeh D, Nguyen TH, Pintacuda G, Postel S, van Raaij MJ, Roversi P, Shimon A, Singh AK, Sundberg EJ, Tars K, Zitzmann N, Schwede T. (2018). Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). Proteins 86 (S1), 27-50. doi: 10.1002/prot.25392. PMID: 2896053 2016: Kryshtafovych A, Moult J, Baslé A, Burgin A, Craig TK, Edwards RA, Fass D, Hartmann MD, Korycinski M, Lewis RJ, Lorimer D, Lupas AN, Newman J, Peat TS, Piepenbrink KH, Prahlad J, van Raaij MJ, Rohwer F, Segall AM, Seguritan V, Sundberg EJ, Singh AK, Wilson MA, Schwede T. (2016). Some of the most interesting CASP11 targets through the eyes of their authors. Proteins 84 (S1), 34-50. doi: 10.1002/prot.24942. PMID: 26473983 2014: Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C, Herzberg O, Lorimer D, Luecke H, Ma X, Nelson DC, van Raaij MJ, Rohwer F, Segall A, Seguritan V, Zeth K, Schwede T. (2014). Challenging the state-of-the-art in protein structure prediction: Highlights of experimental target structures for the 10th critical assessment of techniques for protein structure prediction experiment CASP10. Proteins 82 (S2), 26-42. doi: 10.1002/prot.24489. PMID: 2431898 2011: Kryshtafovych A, Moult J, Bartual SG, Bazan JF, Berman H, Casteel DE, Christodoulou E, Everett JK, Hausmann J, Heidebrecht T, Hills T, Hui R, Hunt JF, Seetharaman J, Joachimiak A, Kennedy MA, Kim C, Lingel A, Michalska K, Montelione GT, Otero JM, Perrakis A, Pizarro JC, van Raaij MJ, Ramelot TA, Rousseau F, Tong L, Wernimont AK, Young J, Schwede T. (2011). Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. Proteins 79 (S10), 6-20. doi: 10.1002/prot.23196. PMID: 2202078 Posted on behalf of the CASP organizing committee: John Moult, University of Maryland, USA Krzysztof Fidelis, University of California, Davis, USA Andriy Kryshtafovych, University of California, Davis USA Torsten Schwede, University of Basel, Switzerland

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R-factor expectations when translational pseudo symmetry is present
by Tanner, John J. 17 Apr '18

17 Apr '18

Dear PhenixBB, We have a crystal form that xtriage flags as having strong translational pseudo symmetry (Patterson peak 57% the height of the origin peak, p-value = 3E-5). The space group is P21212. We can solve the structure with MR and refine to R=0.233 and R-free =0.276 at 2.25 Angstrom resolution. The maps look very good, but do not suggest major additional modeling that could be done to improve the structure and lower the R-factors. I know that one expects the R-factors from refinement to be higher when TPS is present, but my question is how high is too high? Has anyone done a study that shows the expectations for R-factors when TPS is present? Thanks, Jack John J. Tanner Interim Chair, Department of Biochemistry Professor of Biochemistry and Chemistry Department of Biochemistry University of Missouri-Columbia 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-5635 Email: tannerjj(a)missouri.edu<mailto:[email protected]> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A

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Trouble running getting ERRASER to run
by Shintaro Aibara 17 Apr '18

17 Apr '18

*Dear PhenixBB,* *I am trying to get ERRASER to run and am struggling a bit. I was wondering if somebody could point me in the right way. Apologies if this has been asked before - my Google-Fu is inadequate.* *Phenix Version: dev-3092* *Rosetta Version: 2018.09.60072* *I built rosetta using scons as per the instructions online and fired rosetta.build_phenix_interface with no errors. I've identified that the erraser directory lives in main/source/src/apps/public/ERRASER and accordingly set my environmental variables.* *Being fairly clunky around the linux environment, I am probably doing something very silly. Any help would be much appreciated.* *Best wishes,* *Shintaro* *When I try to run erraser from the phenix GUI I am greeted by this error message:* TypeError : __init__() takes at least 3 arguments (1 given) Traceback (most recent call last): File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/wxGUI2/App.py", line 784, in OnTimer self.run_manager.update(update_backgrounded=False) File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/wxGUI2/ProcessControl.py", line 213, in update process.update() File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/wxGUI2/ProcessControl.py", line 136, in update self._process.update() File "/home/saibara/software/phenix/phenix-dev-3092/modules/cctbx_project/libtbx/runtime_utils.py", line 306, in update (error, traceback_info) = easy_pickle.load(self.error_file) File "/home/saibara/software/phenix/phenix-dev-3092/modules/cctbx_project/libtbx/easy_pickle.py", line 80, in load return cPickle.loads(_open(file_name, "rb").read()) TypeError: __init__() takes at least 3 arguments (1 given) *Alternatively if I try to fire phenix.erraser through the command line, I get something like this:* Running ERRASER Rosetta app... ################################### Path to ERRASER: /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/apps/public/ERRASER ERROR: Assertion `scorefxn_->get_weight( cart_bonded ) > 0` failed. ERROR:: Exit from: src/protocols/rna/movers/ErraserMinimizerMover.cc line: 238 BACKTRACE: /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x2ea) [0x7f3e2b7798fa] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/ libprotocols_d.6.so(protocols::rna::movers::ErraserMinimizerMover::i_want_this_atom_to_move(core::chemical::ResidueType const&, unsigned long const&)+0x92) [0x7f3e34c17062] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/ libprotocols_d.6.so(protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry(core::kinematics::MoveMap&, core::pose::Pose&, ObjexxFCL::FArray1D<bool>&, std::set<unsigned long, std::less<unsigned long>, std::allocator<unsigned long> > const&)+0x20a) [0x7f3e34c1771a] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/ libprotocols_d.6.so(protocols::rna::movers::ErraserMinimizerMover::apply(core::pose::Pose&)+0x2020) [0x7f3e34c20f70] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/ libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xbed) [0x7f3e344cc9bd] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/ libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x166) [0x7f3e344cedc6] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/ libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x57) [0x7f3e344b4d67] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease() [0x40480e] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease() [0x4037b1] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7f3e32bdc830] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease() [0x4045b9] Traceback (most recent call last): File "/home/saibara/software/phenix/phenix-dev-3092/build/../modules/phenix/phenix/command_line/erraser.py", line 14, in <module> erraser_run=phenix.erraser.erraser.erraser(args=sys.argv[1:]) File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/phenix/erraser/erraser.py", line 349, in __init__ self.run(params,out=out) File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/phenix/erraser/erraser.py", line 459, in run erraser(option) File "/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 99, in erraser erraser_minimize( minimize_option ) #full_struct_slice_and_minimize( minimize_option ) File "/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 478, in erraser_minimize subprocess_call(command, sys.stdout, sys.stderr) File "/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/apps/public/ERRASER/erraser_util.py", line 107, in subprocess_call subprocess.check_call(command, shell=True, stdout = out_channel, stderr = err_channel) File "/home/saibara/software/phenix/phenix-dev-3092/base/lib/python2.7/subprocess.py", line 186, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease -database /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/database/ -s /home/saibara/Phenix/hsmitoribo_drug/rnaonly_erraser_temp/minimize_0.pdb -score:weights stepwise/rna/rna_hires_elec_dens_FCC2012 -score:rna_torsion_potential FCC2012_RNA11_based_new -rna::corrected_geo true -rna::erraser::rna_prot_erraser false -rna::vary_geometry true -constrain_P true -attempt_pyrimidine_flip false -rna::erraser::skip_minimize false -chemical:enlarge_H_lj false -in:guarantee_no_DNA false -out:file:write_pdb_link_records true -scale_d 100 -scale_theta 10 -stepwise:rna:o2prime_legacy_mode true -use_2prime_OH_potential false -edensity:mapfile /home/saibara/Phenix/hsmitoribo_drug/cheatmap.ccp4 -edensity:mapreso 3.0 -edensity:realign no -graphics false -skip_connect_info true ' returned non-zero exit status 255

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