- phenixbb - phenix-online.org

European Crystallography Meeting Oviedo; Neutron Macromolecular Crystallography Satellite Meeting
by John R Helliwell 09 May '18

09 May '18

Dear Colleagues, We draw your attention to the following meeting in Oviedo, Spain in August:- https://ecm31.ecanews.org/en/neutron-macromolecular-crystallography.php Best wishes, John and Matthew Emeritus Professor John R Helliwell DSc; Dr Matthew Blakeley, Institut Laue Langevin.

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Phenix.rosetta build Ubuntu 16.04
by Joseph Brock 08 May '18

08 May '18

Dear phenix community, I am trying to get phenix to run with rosetta on my Ubuntu 16.04 station. I am running the latest official phenix version (phenix-1.13-2998) and and compiled rosetta 3.7 (2016.32.58837) using scons as described: https://www.phenix-online.org/documentation/reference/rosetta_install.html https://www.rosettacommons.org/docs/latest/build_documentation/Build-Docume… Then ran rosetta.build_phenix_interface. All went without error but running rosetta.run_tests then gave the segmentation fault below. Defining variables as suggested did not help. I found a similar question in the phenixbb archives but no resolution: http://www.phenix-online.org/pipermail/phenixbb/2013-October/020274.html Any suggestions on how to move forward greatly appreciated! Cheers, Joseph. _________________________________________________________________________________________________________ Segmentation fault (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. Traceback (most recent call last): File "/usr/local/phenix-1.13-2998/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 305, in <module> run(sys.argv[1:], create_dir=True) File "/usr/local/phenix-1.13-2998/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run debug=params.output.debug) File "/usr/local/phenix-1.13-2998/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__ self.run_jobs() File "/usr/local/phenix-1.13-2998/modules/phenix/phenix/rosetta/refine.py", line 388, in run_jobs check_result(result) File "/usr/local/phenix-1.13-2998/modules/phenix/phenix/rosetta/refine.py", line 379, in check_result raise RuntimeError("Aborted due to error in job %d." % result.job_id) RuntimeError: Aborted due to error in job 1. Joseph S. Brock | PhD Researcher Drew Lab Department of Biochemistry and Biophysics Stockholm University

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phenix server down?
by Murpholino Peligro 02 May '18

02 May '18

Is the phenix server down? I cannot access the following links http://www.phenix-online.org/documentation https://www.phenix-online.org/download/phenix/release/ :(

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Introducing ISOLDE
by Tristan Croll 01 May '18

01 May '18

Dear members of the structural biology community, It is with great pleasure that I announce the release of version 1.0b1 of ISOLDE, a new, free for academic/nonprofit use, environment for interactive rebuilding of macromolecular models against low-medium resolution experimental crystallographic or cryo-EM maps. A paper describing ISOLDE is online at http://scripts.iucr.org/cgi-bin/paper?S2059798318002425, and you can also get an overview from my demonstration video at https://www.youtube.com/watch?v=limaUsNAVL8. In brief, though, ISOLDE is designed to help overcome the substantial challenge involved in building high-quality models into “difficult” maps (e.g. those with worse than 3Å resolution) by re imagining the task as one akin to interacting with a real, “living” molecule. At its heart is the use of interactive molecular dynamics: all atoms feel van der Waals and electrostatic interactions with their neighbours as you interact with them, avoiding clashes and constantly settling towards their nearest low-energy state. In addition to this, ISOLDE helps interpret what you're looking at by performing real-time rotamer, Ramachandran and peptide plane validation, flagging up potential problems directly on the model to give you instant feedback on the results of your actions. Specific features: - support for protein, nucleic acid, water and some small molecules/ions (with substantially expanded support to come in later versions) - start an interactive simulation covering anything from a few residues to your entire model (depending on your hardware) at the click of a button - “always-on” validation updates every time coordinates change (results are shown directly as markup on the model itself, and also accessible via more traditional tables/plots) - Interactively apply peptide plane or cis/trans flips and add/remove position, distance, rotamer and secondary structure restraints via a simple graphical interface - Smoothly shift any continuous stretch of backbone forward/backward along the chain to easily recover from register shift errors - Save a checkpoint in a running simulation and return to it with a button click, allowing you to experiment with tricky regions without fear - Real-time visualisation of crystal symmetry contacts: when the master atoms move, they move. - One-button masking of maps to cover any arbitrary atom selection – particularly useful for diagnosing large-scale problems. - Extensive GUI and API documentation, available by clicking the “Help” button in the ISOLDE GUI window. ISOLDE is built as a plugin to UCSF ChimeraX (http://preview.cgl.ucsf.edu/chimerax/download.html) and is currently available for modern Linux distros and MacOS, and can be installed from within ChimeraX via its ToolShed (Tools/More Tools...). It should run on any Linux version that supports ChimeraX itself. NOTE: due to some recent changes in the ChimeraX API, the current build will only work with the ChimeraX 0.6 release (not the version 0.7 daily builds). In terms of hardware, ISOLDE is designed based on the understanding that not everybody has access to high-performance computing facilities, so its minimum requirements are as modest as possible. The most important requirement is a GPU capable of OpenCL 1.2 or CUDA processing. My “go-to” machine for performance testing is a 2016-model gaming laptop equipped with a Nvidia GTX 1070 GPU – this achieves ~20 coordinate updates and >30 graphics updates per second with live validation on the included 229-residue demo model, indistinguishable from (or slightly faster than) my Xeon workstation. At the other end of the scale, it runs at usable speeds on my MacBook Air for simulations of a few dozen residues, sufficient for many tasks. I hope you find it useful, and enjoy using it as much as I've enjoyed making it. The MolProbity score to beat on the demo model is 1.02 (after refinement in your favourite package – ID is in the PDB header so you can download reflections from the wwPDB), and bonus points if you can identify the mystery ligand (I can't). If you recognise it as your model I apologise – I picked it out at random, I swear! Best regards, Tristan

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DNA pucker
by Dyda 30 Apr '18

30 Apr '18

Hi, Is it possible and if so how to change the pucker restraint for a particular DNA nucleotide from C2'-endo to C3'-endo in phenix.refine? I have a problem with a terminal nucleotide that is in an active site and the current C2'-endo doesn't seem consistent with the 2Fo-Fc map. Thanks for your help. [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710(a)mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m

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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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