- phenixbb - phenix-online.org

real space refine ADPs
by Leonid Sazanov 08 Oct '24

08 Oct '24

Hi, according to online description phenix.real_space_refine should refine only group ADPs per residue. However, in practice after the run with ADP included in strategy the recent versions refine individual B-factors per atom. They seem to look OK, but I wonder if this is a beta feature or fully implemented by now? Many thanks Leonid -- Prof. Leonid Sazanov FRS Institute of Science and Technology Austria (ISTA) Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: sazanov(a)ist.ac.at

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new BUILT of XDS
by kay.diederichs＠uni-konstanz.de 04 Oct '24

04 Oct '24

Dear XDS users in the Phenix community, as reported by users, and confirmed in a larger-scale comparison by GlobalPhasing, the BUILT=20240723 of XDS Version 20240630 leads to problems for some datasets when compared with (the expired) XDS Version 20230630. (it may be better than the 20230630 version for other datasets!). An improved BUILT=20241002 of the 20240630 version is available (all platforms) from https://xds.mr.mpg.de/html_doc/downloading.html for non-commercial (academic) users (commercial users have their own arrangements). In my/our testing, it is at least as good as version 20230630, and often better. Please install and use this instead of BUILT=20240723. If you still find deficiencies, please contact me or Wolfgang Kabsch - but be prepared to share the raw data (confidentially, of course). To enable comparisons, the old XDS version 20230630 was re-released for Linux by Wolfgang Kabsch with expiration date 2025-Mar-31; the link to its XDS_old.tar.gz is at https://xds.mr.mpg.de/ . Best wishes, Kay

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Registration now open for CCP4 Study Weekend 2025 - Using software, AI and other methods to advance macromolecular models
by Karen McIntyre - STFC UKRI 03 Oct '24

03 Oct '24

Dear all, Registration is now open for the 2025 CCP4 study weekend entitled " Using software, AI and other methods to advance macromolecular models". This year the CCP4 Study Weekend will be held as a hybrid event from the 7th to 9th January 2025, enabling people to choose whether to attend in-person or virtually. The in-person event will be held at the East Midlands Conference Centre, Nottingham, UK. We would like to invite you to another iteration of the ever-popular CCP4 Study Weekend - to start the year 2025 with a lot of fresh ideas, new insights and (hopefully) new friends and contacts to boost. As always it will be an eclectic mix of bleeding-edge science, in-depth presentations, discussion panel, poster-sessions, hands-on tutorials and plenty of opportunities for social interactions. For full details, programme, logistics and registration, please visit the Study Weekend website<https://studyweekend.ccp4.ac.uk/>. There is no better way to start 2025 than to put participation in that exciting meeting at the top of your "New Year's Resolutions" list! Key Dates: * Early bird registration final date: 11 November 2024; * Standard Student bursaries are open to all students registering during early bird period i.e. now until 11 November which cover the cost of registration plus one night accommodation in halls (1 night in hotel will be subsidised for those students choosing to stay in the hotel); * Travel bursaries are available for students and young postdocs studying at overseas labs to help cover cost of travel to UK. The deadline for applications is 31 October 2024; * Registration for in-person delegates closes 4 December 2023 (or earlier if in-person places sell out although you will be able to join the in-person waitlist). * Registration for virtual delegates will close 9 January 2025. Key Timings Diamond MX user meeting will start at 11:00 on 7TH January 2025 CCP4 study weekend 2025 will start at ~17:30 on 7th January 2025 the event will finish at ~16:30 on 9th January 2025 We hope to see you there! Scientific Organisers: Elke De Zitter (Institut de Biologie Structurale, FRANCE) Deborah Harrus (EMBL-EBI, UK) Dorothee Liebschner (Lawrence Berkeley National Laboratory, USA) Administrative Organisers: Karen McIntyre (CCP4, UK)

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ResolveCryoEM inputs
by Josh Cofsky 17 Sep '24

17 Sep '24

Hi, I'm attempting to run ResolveCryoEM, and I have a few questions about setting the job up correctly. My half-maps were reconstructed with C4 symmetry to ~2 Å (CryoSPARC), and my model was refined into the density with the "Ncs constraints" box checked (Phenix RSR). My sample is a protein-DNA complex (4 copies of a protein protomer, 4 copies of a ssDNA protomer). I'm running Phenix 1.21.1-5286-000 (the latest installation provided by SBGrid). In the first version of the run, I only supplied the two half-map files and a seq file. Question 1: My current seq.dat file looks like this (as mentioned previously in the forum, I was getting errors when I tried the version where my seq.dat file has only 1 protomer and I set the number of copies to 4 in the GUI field "Copies of sequence file in map"): >protein_protomer1 MGSRSG... >protein_protomer2 MGSRSG... >protein_protomer3 MGSRSG... >protein_protomer4 MGSRSG... >DNA_protomer1 AAAAAA >DNA_protomer2 AAAAAA >DNA_protomer3 AAAAAA >DNA_protomer4 AAAAAA Currently, Phenix is reading in the "AAAAAA" as a protein chain ("Chain types considered: PROTEIN"). How do I tell Phenix that those are deoxyadenosines, not alanines? Question 2: Is Phenix automatically detecting the C4 symmetry and density-modifying with that constraint? The resulting map looks symmetric in the noise, but I don't see anything in the log suggesting that it knows the symmetry. Here are some settings from the log that seem relevant (all left to default values): refine_symmetry_in_denmod = True use_symmetry_in_denmod = False symmetry_in_denmod_last_cycle_only = True fraction_ncs = None I attempted to supply a symmetry file (the output of a MapSymmetry job on the full map = "symmetry_from_map.ncs_spec"), but the file fails to load into the input ("Phenix error: Phenix did not recognize the file type for ****/symmetry_from_map.ncs_spec"). Question 3: A part of my protein is disordered and does not appear in the cryo-EM density (and was thus left unmodeled). Is it correct to leave that piece out of the seq.dat file? Question 4: If I include a model in the input, Phenix demands a symmetry file, but I couldn't get my symmetry file to load as explained above. What is the symmetry file supposed to look like? Thank you! -Josh

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Ordered solvent in phenix.refine
by Oliver H. Weiergräber 11 Sep '24

11 Sep '24

Hello, after switching from version 1.20 to 1.21, I noticed that the updated list of waters generated by the ordered_solvent option in phenix.refine is no longer numbered sequentially; it seems a final re-numbering step is now skipped. Is this intentional? Of course it can be advantageous to keep waters from changing their numbers, e.g. if they are part of occupancy groups. On a related note, is there a mechanism to protect certain "important" waters from being deleted while all the rest is updated as usual? One obvious option would be a dedicated chain ID, but afaik phenix.refine accepts a chain ID for output but not for input waters ... Best regards, Oliver ================================================== Prof. Oliver H. Weiergräber Institute of Biological Information Processing IBI-7: Structural Biochemistry Forschungszentrum Jülich 52425 Jülich, Germany Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ==================================================

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Phenix version 1.21.2 released
by Paul Adams 05 Sep '24

05 Sep '24

The Phenix developers are pleased to announce that version 1.21.2 of Phenix is now available (build 1.21.2-5419). Binary installers for Linux, Mac OSX, and Windows (under Windows Subsystem for Linux), and the source installer, are available at the download site: http://phenix-online.org/download Highlights for this bug fix 1.21.2 version of Phenix include: - Fix issue where X-ray data parameters (e.g. resolution) are not used - Fix issue where non-default map coefficient parameters cause map names to be numbered - Fix issue where phenix.refine parameter diff could not be saved - Differences in DataManager PHIL are now included when using getting non-default parameters - Additional filtering is applied to Miller array selections to avoid ambiguity - The const_shrink_donor_acceptor default has been changed from 0.6 to 0.0 Please note that this publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix has been funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. The maintenance and distribution of Phenix is currently funded by the National Institute of General Medical Sciences (NIH) under grant R24-GM141254. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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phenix quantum interface with Orca
by Guenter Fritz 30 Aug '24

30 Aug '24

Dear Phenix developers, I am currently trying the quantum interface on several cases. on https://phenix-online.org/documentation/reference/quantum_interface.html you write that one can also implement Orca. I am a very basic (not really experienced) Orca user, but nevertheless I would be happy to try it, since I have Orca installed on my , Ubuntu or Rocky) Is there a phenix variable that I have to point to Orca or can I set usage of orca in the .phil file with the package item? Thanks a lot and best regards, Guenter

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problem launching Phenix 1.21.1-5286 under Debian 12 Linux
by cparthier＠googlemail.com 29 Aug '24

29 Aug '24

Hi, I'm having problems running the current Phenix release (1.21.1-5286, but also earlier versions) on a fresh setup of Debian GNU/Linux 12 (bookworm, kernel 6.1.0-23-amd64). Phenix binaries have been installed on an NFS share ("hd1"), hostname is "phe". This is the error output: ----------------------------- phe:~> source /hd1/SOFT64/phenix-1.21.1-5286/phenix_env.csh phe:~> phenix Gtk-Message: 13:29:49.433: Failed to load module "canberra-gtk-module" Error in sys.excepthook: Traceback (most recent call last): File "/nfs/hd1/SOFT64/phenix-1.21.1-5286/modules/phenix/wxGUI2/App.py", line 961, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/nfs/hd1/SOFT64/phenix-1.21.1-5286/modules/phenix/wxGUI2/Error.py", line 76, in show_exception_dialog if (app.bug_timer.IsRunning() is False): AttributeError: 'PhenixApp' object has no attribute 'bug_timer' Original exception was: Traceback (most recent call last): File "/nfs/hd1/SOFT64/phenix-1.21.1-5286/build/../modules/phenix/wxGUI2/command_line/main.py", line 34, in <module> run(sys.argv[1:]) File "/nfs/hd1/SOFT64/phenix-1.21.1-5286/build/../modules/phenix/wxGUI2/command_line/main.py", line 28, in run wxapp = App.PhenixApp(args) File "/nfs/hd1/SOFT64/phenix-1.21.1-5286/modules/phenix/wxGUI2/App.py", line 84, in __init__ wx.App.__init__(self, 0) File "/nfs/hd1/SOFT64/phenix-1.21.1-5286/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8628, in __init__ self._BootstrapApp() File "/nfs/hd1/SOFT64/phenix-1.21.1-5286/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8196, in _BootstrapApp return _core_.PyApp__BootstrapApp(*args, **kwargs) File "/nfs/hd1/SOFT64/phenix-1.21.1-5286/modules/phenix/wxGUI2/App.py", line 118, in OnInit show_splash_screen(timeout=2000) File "/nfs/hd1/SOFT64/phenix-1.21.1-5286/modules/phenix/wxGUI2/App.py", line 1015, in show_splash_screen dlg,-1,citations.format_citation(citations.citations_db.get("phenix"))) File "/nfs/hd1/SOFT64/phenix-1.21.1-5286/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_controls.py", line 997, in __init__ _controls_.StaticText_swiginit(self,_controls_.new_StaticText(*args, **kwargs)) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 40: ordinal not in range(128) -------------------- Phenix does not run. The ""canberra-gtk-module" was missing first, but installing it did not prevent the error. Any hint what could be wrong? Thanks, Christoph

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Haskris R175 chiller available
by Jonathan Ruprecht 23 Aug '24

23 Aug '24

Dear bulletin board members, The MRC Mitochondrial Biology Unit in Cambridge, UK, has a Haskris R175-FEI-BHKL(RS) 3.2kVA air-cooled recirculating chiller (with hot gas bypass) that is now surplus to our requirements and available free of charge (the new owner would be asked to pay for transport). This was previously used to supply chilled water to a TEM. Please direct any enquiries to David Pate, MBU Laboratory Manager, ddp10(a)cam.ac.uk. Best wishes, Jonathan Ruprecht -- Dr Jonathan Ruprecht MRC Mitochondrial Biology Unit University of Cambridge Keith Peters Building Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY

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Presence of negative density in Sim Omit map
by Renuka Kadirvelraj 12 Aug '24

12 Aug '24

Presence of negative density in Sim Omit map Hi Phenixbb, We would appreciate your advice regarding an odd problem that has cropped up with one of our crystal structures. We have a protein structure in space group P6(3)22 at 2.1 A resolution and in the final refinement stages with Rwork of 0.20 and Rfree of 0.22. When we ran simulated annealing to rebuild an outlier Lysine residue in a loop, the Sim Omit map showed the positive density expected from the omission of the loop (contour level 3 sigma, colored green in attached pics). However, flanking the positive density, there is a complimentary negative density (in red). We are puzzled as to the cause of the appearance of the negative density. Can you help us? Many thanks, Renu --------------------------------------------- Renu Kadirvelraj, Ph.D. Research Scientist A428, Biochemistry and Molecular Biology 120, East Green Street University of Georgia Athens, GA 30602 Tel: (706) 583 0303

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