August 2024 - phenixbb - phenix-online.org

RapiData at SSRL 2024
by Smith, Clyde 17 Nov '24

17 Nov '24

Hi everyone, Applications are now open for the 2024 edition of RapiData at SSRL. RapiData is a practical course in macromolecular X-ray diffraction data collection, data processing and structure solution. The aim of the RapiData course is to educate and train young scientists in data collection and processing methods at synchrotron beamlines, using state-of-the-art software and instrumentation. The course will be held at the Stanford Synchrotron Radiation Lightsource (SSRL) located on the SLAC National Accelerator Laboratory campus in Menlo Park, CA, from April 29 to May 4, 2024. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on the following topics: Specimen preparation, Data collection strategies, X-ray light sources, X-ray detectors, Data reduction, Structure solution by MAD, SAD and Molecular Replacement, Complementary methods (spectroscopy and small angle scattering) Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2024/ and use the links on the "Application and Registration" page to apply for the course. The application deadline is January 31, 2024. Successful applicants will be notified early in February 2024 and invited to register and book accommodation at SLAC Stanford Guesthouse at that time. A limited amount of support funding may be available. Please direct questions to Silvia Russi (srussi(a)slac.stanford.edu) or Clyde Smith (csmith(a)slac.stanford.edu).

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Re: [phenixbb] red blobs (Andrea Smith)
by Kay Diederichs 31 Oct '24

31 Oct '24

Hi Andrea, in your case, phenix.refine seems to fill bulk solvent into volumes that are not actually filled by solvent. It might help to optimize the mask, see https://phenix-online.org/documentation/reference/refinement.html#bulk-solv… "6. Mask parameters". Best, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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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 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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Maatel HC1c humidity controller available
by Jonathan Ruprecht 07 Aug '24

07 Aug '24

Dear bulletin board members, The MRC Mitochondrial Biology Unit in Cambridge, UK, has a Maatel HC1c humidity controller, together with the ancilliary components necessary to make a crystal dehydration rig, including a Nikon SMZ800 microscope, that is now surplus to our requirements and available free of charge (the new owner would be asked to pay for shipping). This was purchased in 2010, last used in approximately 2017 and is thought to be a working system. 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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phenix.refine command line: what to change on the subsequent def file to point to the desired input pdb
by Alejandro Buschiazzo 02 Aug '24

02 Aug '24

Dear phenix users/developers Some time ago there were several modifications on the names/specifications of important parameters/options (such as miller_array for structure factor files, etc) Running phenix.refine by command lines (no gui) is my favorite, and I am now running into several difficulties: 1- what’s the difference between miller_array and default_miller_array; or model and default_model? 2- what’s the precise definition of phil_files and default_phil? What to change if I manually edit my .eff? 3- how should I use the new automatically created .def file for subsequent refinement cycles after I’ve manually rebuilt (I need to point to the new pdb input file: I usually screw this up, can’t seem to use the newly created .def as my starting instructions file anymore, it complains that I have problems in the right definition of the input pdb, or too many models...) 4- I often fall into a loop where by default newly created .eff files include a dry_run=true option (e.g. when I deliberately tell phenix.refine to overwrite previous .eff files) Thanks a lot for clarifying on these issues: and sorry, for I couldn’t find obvious answers to them in the documentation (probably my fault!!) Also, I am using phenix v 1.21.1-5286 (on a Sonoma MacOS laptop) With best wishes Alejandro

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