- phenixbb - phenix-online.org

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

17 Jan '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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Phenix does not start
by Cygler, Miroslaw 11 Jan '24

11 Jan '24

Hi, I have recently upgraded my MacBook running M1 processor to the Sonoma 14.2.1 operating system. Now, when I tried to start Phenix GUI, a message pops up: “python quit unexpectedly” and guy does not open. Any advice would be helpful. Regards, Mirek

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Secondary structure weights for realspace refinement
by Reza Khayat 10 Jan '24

10 Jan '24

Hi, I hope all is well. Is there a way to alter the weights for secondary structure restraints? Thanks. Best wishes Reza Reza Khayat, PhD City College of New York Associate Professor Department of Chemistry and Biochemistry Co-Director NIH G-RISE program

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Input from the community for panel session: Crystallography is Dead! Long Live Crystallography!
by Nicholas Pearce 02 Jan '24

02 Jan '24

Hello, and happy new year! [and absolutely no apologies for cross-posting 😉] Tomorrow evening, we will have a panel discussion at the CCP4 study weekend about the future of crystallography, called “Crystallography is Dead. Long Live Crystallography!” [https://en.wikipedia.org/wiki/The_king_is_dead,_long_live_the_king]. Whether you’re attending the CCP4SW or not, we want to hear from the community about your thoughts on the subject (see the blurb below), so that we can discuss things the community is most interested in! if you have a few minutes, please do fill in the form (all questions are optional): https://forms.office.com/e/3K5qSMNpYh. Thanks, and looking forward to seeing some of you very soon! Your friendly neighbourhood scientific organisation team, Nicholas Pearce, Helen Ginn, and Clemens Vonrhein Blurb: In this session, we will discuss the current state and the future of crystallographic experiments in the context of structural biology: * what are the unconfronted problems that the field still faces? * what problems are now essentially solved? * where should future method development be focussed? * what challenges are emerging from new experimental developments? * do new experiments provide new perspectives on old problems? Inevitably, this will include discussion of whether these challenges are likely to be addressed by the application of recent advances in AI, and, with the continued developments in cryoEM, what is crystallography's role as a part of the structural biologist's toolbox? Panel Chair: Elspeth Garman Panel Members: Dave Brown, Arwen Pearson, Ashwin Chari Please submit questions for consideration during the panel discussion using the form below! and we look forward to seeing you on 3rd Jan! Some of the questions are asked mischievously - you are welcome to have some fun with your answers! All questions are optional! https://forms.office.com/e/3K5qSMNpYh

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Fwd: Phenix installation on macOS 14 Sonoma
by Billy Poon 31 Dec '23

31 Dec '23

Sorry if this is a duplicate, but I'm not sure if my response got sent to the bulletin board correctly. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org ---------- Forwarded message --------- From: Billy Poon <BKPoon(a)lbl.gov> Date: Sun, Dec 31, 2023 at 6:29 PM Subject: Re: [phenixbb] Phenix installation on macOS 14 Sonoma To: Klureza, Maggie <mklureza(a)g.harvard.edu> Cc: <phenixbb(a)phenix-online.org> Hi Maggie, Can you run the script from inside the sonoma_fix directory? That is, 1) Extract sonoma_fix.tar.gz 2) cd sonoma_fix 3) sudo ./fix_wxpython.sh /Applications/phenix-1.19.2-4158 Inside the sonoma_fix directory, there should be a "bin" directory with conda.exe. The installed versions of Phenix do not come with conda. The fix comes with a standalone version of conda that can modify the Phenix environment with the dependencies. Let us know if it's still not working. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org On Sun, Dec 31, 2023 at 5:49 PM Klureza, Maggie <mklureza(a)g.harvard.edu> wrote: > Hi all, > > Reviving this thread (or trying to, anyway - TBD if I can successfully > reply to a thread begun before I'd joined the phenixbb list!), I recently > updated my Mac OS to 14/Sonoma, and am now also having issues getting > Phenix to work. > > As directed on the installers page > <https://phenix-online.org/download/phenix/release/>, I downloaded the > supplied fix <https://phenix-online.org/download/sonoma_fix.tar.gz>, > extracted the tarball, and ran that code as `sudo > Downloads/sonoma_fix/fix_wxpython.sh /Applications/phenix-1.19.2-4158`. > This was the resulting output/error I got: > > Password: > Removing old version of wxPython > ================================ > Downloads/sonoma_fix/fix_wxpython.sh: line 36: ./bin/conda.exe: No such > file or directory > > Installing new version of wxPython > ================================== > Downloads/sonoma_fix/fix_wxpython.sh: line 42: ./bin/conda.exe: No such > file or directory > > The wxPython package has been updated in /Applications/phenix-1.20.1-4487. > > > Sure enough, when I went to my phenix installation and looked in > conda_base/bin, there was no file named `conda.exe` present. This was true > for both my prior installation (phenix-1.19.2-4158) and when I tried a > newly downloaded version (phenix-1.20.1-4487). > > Can anyone tell me how I get that conda.exe file included with the Phenix > download/how else I might be able to run Phenix with this OS? > > (I sent an email about this to help(a)phenix-online.org before thinking to > hunt through the phenixbb archive, so apologies to whoever checks that > email and is getting this message twice!) > > Many thanks, > Maggie > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

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Re: [phenixbb] Phenix installation on macOS 14 Sonoma
by Klureza, Maggie 31 Dec '23

31 Dec '23

Hi all, Reviving this thread (or trying to, anyway - TBD if I can successfully reply to a thread begun before I'd joined the phenixbb list!), I recently updated my Mac OS to 14/Sonoma, and am now also having issues getting Phenix to work. As directed on the installers page <https://phenix-online.org/download/phenix/release/>, I downloaded the supplied fix <https://phenix-online.org/download/sonoma_fix.tar.gz>, extracted the tarball, and ran that code as `sudo Downloads/sonoma_fix/fix_wxpython.sh /Applications/phenix-1.19.2-4158`. This was the resulting output/error I got: Password: Removing old version of wxPython ================================ Downloads/sonoma_fix/fix_wxpython.sh: line 36: ./bin/conda.exe: No such file or directory Installing new version of wxPython ================================== Downloads/sonoma_fix/fix_wxpython.sh: line 42: ./bin/conda.exe: No such file or directory The wxPython package has been updated in /Applications/phenix-1.20.1-4487. Sure enough, when I went to my phenix installation and looked in conda_base/bin, there was no file named `conda.exe` present. This was true for both my prior installation (phenix-1.19.2-4158) and when I tried a newly downloaded version (phenix-1.20.1-4487). Can anyone tell me how I get that conda.exe file included with the Phenix download/how else I might be able to run Phenix with this OS? (I sent an email about this to help(a)phenix-online.org before thinking to hunt through the phenixbb archive, so apologies to whoever checks that email and is getting this message twice!) Many thanks, Maggie

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geometrical restraints between symmetry related chains
by Jorge Iulek 29 Dec '23

29 Dec '23

Dear all, I am working currently on a structure that should be "peptide bond" between chains, but the "second" part of the chain is in a symmetry related peer. Numbering is continuous and there are justifications to why the chains are separately named with different chain ID's. By the way, this "connection" is "full of glycines" so a kind of flexible, but a continuous stretch can be seen at "reasonable" density (and despite low resolution). To better explain, say I have chain C residue x to be bound to chain K, at symm operation -x-1,y-1/2,-z-1/2, residue x + 1. I would prefer to really refine the presence of these "connecting" glycines, of course with due geometrical restraints imposed (precious at this low resolution). phenix.refine offers: refinement.geometry_restraints.edits at bond with the possibility to indicate the symmetry_operation for the "second atom" within the bond. But this "symmetry_operation" indication is not available (?) for the other geometry_restraints edits, like angle, dihedral, etc. (eventually, planarity might also make easier). Do I miss anything here? Currently, I see 3 possibilities: a) somehow (how?) I can add angle, dihedral restraints in involving chains in symmetry related operations b) I bring the symmetry related chain to its non "symmetry related" position and change chains names/residues ID, etc., so I go into this go/return of naming at each step of the refinement work/analysis c) I add "extra" ( + - like alternate conformation residues) residues to each end of the connection, such that these extra residues will receive due conventional geometrical restraints (as phenix.refine does for contiguous residues in a chain) but I force them to be on the same position (and probably declare 0.5 occupancy for these overlying residues). "a" should be the easiest, if available somehow; "b" would be cumbersome during the refinement/analysis process; "c" seems to be the most complex but maybe the best if it works. Nevertheless, someone might have an easier suggestion. Thanks, Jorge

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Phenix windows distortion windows
by Dmitry Semchonok 28 Dec '23

28 Dec '23

Dear colleagues, I am not sure of the reason, but when I run Phenix, I get the following distortion of the Phenix window. Then, the distortion disappears if I move the cursor somewhere else and click somewhere out of the Phenix window. (please see attachment) Do you know the reasons and how to fix that? Phenix version - 1.21-5187 WSL Windows 11 I will try to 1. roll-back windows drivers 2. update Phenix Kind regards, Dmitry

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Re: [phenixbb] phenixbb Digest, Vol 216, Issue 7 (out of office)
by Elisabeth Laurent 27 Dec '23

27 Dec '23

Thank you for your e-mail. I am out of office until January 2nd, 2024. I will respond to your e-mail as soon as possible upon my return. For urgent matters please contact: bmca(a)boku.ac.at Thank you for your understanding. With kind regards, Elisabeth Laurent >>> <phenixbb-request(a)phenix-online.org> 27.12.23 17:32 >>> Send phenixbb mailing list submissions to phenixbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit http://phenix-online.org/mailman/listinfo/phenixbb or, via email, send a message with subject or body 'help' to phenixbb-request(a)phenix-online.org You can reach the person managing the list at phenixbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. Re: phenix.model_vs_sequence not working as expected (Oleg Sobolev) 2. real space refinement of the model in cryo-EM map (Dmitry Semchonok) 3. Re: real space refinement of the model in cryo-EM map (Pavel Afonine) ---------------------------------------------------------------------- Message: 1 Date: Fri, 22 Dec 2023 11:21:13 -0800 From: Oleg Sobolev <osobolev(a)lbl.gov> To: "Tanner, John J." <TannerJJ(a)missouri.edu> Cc: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: Re: [phenixbb] phenix.model_vs_sequence not working as expected Message-ID: <CADd3otGkgta4heL2mHYB1sfkm_AxEw77Psd7RdS+pGQhjED7dA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi John, Thank you for reporting the issue. I have fixed it. This tool should work again in Phenix builds starting from 5188. Best regards, Oleg Sobolev. On Wed, Dec 20, 2023 at 9:35?AM Tanner, John J. <TannerJJ(a)missouri.edu> wrote: > I?ve noticed that command line phenix.model_vs_sequence does not work in > phenix-1.21rc1-5156. > > > > Here?s the data: > > > > [tannerjj@dizzy pdbs]$ which phenix.model_vs_sequence > > /linux/src/phenix-1.21rc1-5156/build/bin/phenix.model_vs_sequence > > [tannerjj@dizzy pdbs]$ phenix.model_vs_sequence 8DKP.pdb > ../depo/8DKP.fasta > > Traceback (most recent call last): > > File > "/linux/src/phenix-1.21rc1-5156/build/../modules/cctbx_project/mmtbx/command_line/model_vs_sequence.py", > line 75, in <module> > > run(sys.argv[1:]) > > File > "/linux/src/phenix-1.21rc1-5156/build/../modules/cctbx_project/mmtbx/command_line/model_vs_sequence.py", > line 48, in run > > pdb_in = iotbx.pdb.inpu(params.input.pdb_file) > > AttributeError: 'module' object has no attribute 'inpu' > > > > > > It worked fine in phenix-1.20.1-4487: > > > > [tannerjj@dizzy pdbs]$ source /linux/src/phenix-1.20.1-4487/phenix_env.csh > > [tannerjj@dizzy pdbs]$ which phenix.model_vs_sequence > > /linux/src/phenix-1.20.1-4487/build/bin/phenix.model_vs_sequence > > [tannerjj@dizzy pdbs]$ phenix.model_vs_sequence 8DKP.pdb > ../depo/8DKP.fasta > > Skipping non-polymer chain 'A' > > Skipping non-polymer chain 'B' > > Skipping non-polymer chain 'A' > > Skipping non-polymer chain 'B' > > Chain 'A': > > best matching sequence: 8DKP_1|Chains > > sequence identity: 100.00% > > 10 residue(s) missing from PDB chain (3 at start, 1 at end) > > 1 gap(s) in chain > > > > > > PDB file ---QSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHXXXXX > > > |||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGS > > > > > PDB file XGSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX > > > || > > > sequence SGS--------------------------------------------------------- > > > > > PDB file XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMMGEQFVTGETIREA > > > ||||||||||||||| > > > sequence ---------------------------------------------MMGEQFVTGETIREA > > > > > PDB file LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI > > > > > PDB file KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC > > > > > PDB file LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD > > > > > PDB file GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY > > > > > PDB file EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN > > > > > PDB file DPKVSIDELIADPVEVV- > > ||||||||||||||||| > > sequence DPKVSIDELIADPVEVVR > > > > Chain 'B': > > best matching sequence: 8DKP_1|Chains > > sequence identity: 100.00% > > 8 residue(s) missing from PDB chain (0 at start, 1 at end) > > 1 gap(s) in chain > > > > > > PDB file SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHXXXXX > > > ||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGS > > > > > PDB file XXSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX > > > | > > > sequence SGS--------------------------------------------------------- > > > > > PDB file XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMMGEQFVTGETIREA > > > ||||||||||||||| > > > sequence ---------------------------------------------MMGEQFVTGETIREA > > > > > PDB file LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI > > > > > PDB file KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC > > > > > PDB file LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD > > > > > PDB file GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY > > > > > PDB file EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN > > > > > PDB file DPKVSIDELIADPVEVV- > > ||||||||||||||||| > > sequence DPKVSIDELIADPVEVVR > > > > [tannerjj@dizzy pdbs]$ > > > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org >

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real space refinement of the model in cryo-EM map
by Dmitry Semchonok 27 Dec '23

27 Dec '23

Dear colleagues, Does anyone know how to improve the Ramachandran plot Z score (Rama-Z)? Ours seems to be too good (low) 🙂 Is there any cure in Phenix for that? Maybe changing certain parameters/restraints can aid? Thank you. Kind regards, Dmitry

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