- phenixbb - phenix-online.org

treating the water molecules in the model
by Dmitry Semchonok 20 Jan '24

20 Jan '24

Dear colleagues, Please share your experience with how you handle the water molecules. So, we have a refined model and added the water molecules using the Douse protocol. So, should we refine the model again afterwards? Or is the model considered ready? We tried to refine our model with water, but then the water molecules flew away from the places. Please let me know what is the correct way to proceed. Many thanks for considering my request. Sincerely, Dmitry

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General interest: Interoperability of crystallographic data and databases
by John R Helliwell 19 Jan '24

19 Jan '24

Dear Colleagues, I imagine you will be interested in this Feature Article on the "Interoperability of crystallographic data and databases" in the current issue of IUCrJ:- https://journals.iucr.org/m/issues/2024/01/00/lt5064/index.html Best wishes, John Emeritus Professor John R Helliwell DSc

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Post to the email list
by Supeshala Nawarathnage 18 Jan '24

18 Jan '24

Hello, I would like to request to add my email address to your mailing list. My email address is nawa.science(a)gmail.com Thank you. Sincerely, Supeshala Nawarathnage

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Updated links - Phenix version 1.21 released
by Paul Adams 18 Jan '24

18 Jan '24

The Phenix developers are pleased to announce that version 1.21 of Phenix is now available (build 1.21-5207). 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 the 1.21 version of Phenix include: - Likelihood-based docking of models into cryo-EM maps. • Full support for structure determination with AlphaFold models. • New joint X-ray and neutron refinement algorithm. • Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ. Detailed changes are: - Full support for structure determination with AlphaFold models in Phenix GUI - PredictAndBuild X-ray and Cryo-EM structure solution from data and sequences - Phenix AlphaFold server - Video tutorials for prediction, X-ray structure solution and Cryo-EM map interpretation - Cryo-EM tools support ChimeraX visualization - Cryo-EM density modification and anisotropic scaling display local resolution - Tutorials available for automated structure determination with PredictAndBuild - New em_placement and emplace_local tools - likelihood-based docking of models into cryo-EM maps - MOPAC v22 is now distributed with Phenix - Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ - Available in phenix.refine and separate command-line tool, mmtbx.quantum_interface - Defaults to MOPAC's PM6-D3H4 - Higher level QM available via 3rd-party Orca package - Restraints - Approximately 27k of 37k restraints (QM calculated and validated) deployed in the GeoStd - Automated tests for programs in the Phenix GUI - ERRASER no longer supported and removed from installation - Remove rebuild_predicted_model (duplicated by predict_and_build) - JSON output added to MolProbity structure validation scripts 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 is funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. The maintenance and distribution of Phenix is 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 version 1.21 released
by Paul Adams 17 Jan '24

17 Jan '24

The Phenix developers are pleased to announce that version 1.21 of Phenix is now available (build 1.21-5207). 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 the 1.21 version of Phenix include: - Likelihood-based docking of models into cryo-EM maps. • Full support for structure determination with AlphaFold models. • New joint X-ray and neutron refinement algorithm. • Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ. Detailed changes are: - Full support for structure determination with AlphaFold models in Phenix GUI - PredictAndBuild X-ray and Cryo-EM structure solution from data and sequences - Phenix AlphaFold server - Video tutorials for prediction, X-ray structure solution and Cryo-EM map interpretation - Cryo-EM tools support ChimeraX visualization - Cryo-EM density modification and anisotropic scaling display local resolution - Tutorials available for automated structure determination with PredictAndBuild - New em_placement and emplace_local tools - likelihood-based docking of models into cryo-EM maps - MOPAC v22 is now distributed with Phenix - Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ - Available in phenix.refine and separate command-line tool, mmtbx.quantum_interface - Defaults to MOPAC's PM6-D3H4 - Higher level QM available via 3rd-party Orca package - Restraints - Approximately 27k of 37k restraints (QM calculated and validated) deployed in the GeoStd - Automated tests for programs in the Phenix GUI - ERRASER no longer supported and removed from installation - Remove rebuild_predicted_model (duplicated by predict_and_build) - JSON output added to MolProbity structure validation scripts 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 is funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. The maintenance and distribution of Phenix is 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 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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phenix.model_vs_sequence not working as expected
by Tanner, John J. 22 Dec '23

22 Dec '23

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]$

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Two-year postdoctoral position in time-resolved crystallography at IBS in Grenoble
by Elke De Zitter 22 Dec '23

22 Dec '23

Dear all, We have an immediate opening for a two-year postdoctoral researcher in SNaX team of the DYNAMOP group at the Institute for Structural Biology in Grenoble (France). The successful candidate will work on the development and optimization of bio-scavengers towards toxic organophosphorus compounds. To attain this goal, the researcher will use time-resolved crystallography and in silico protein design methods. The position is funded by the French National Research Agency via the University Grenoble Alpes, and is open for a young researcher. Applicants must have obtained a Ph.D. in structural biology, biochemistry, biophysics, physics, chemistry, or a related field, no more than two years before the start of the project. The candidate must show a track-record of publications in peer-reviewed journals, and is expected to be proficient in English and highly motivated to learn new skills. The candidate will work in the multidisciplinary DYNAMOP group and thus needs to be a good team player as well as being capable of working independently. While the research will be carried out in English, non-French-speaking candidates are expected to learn the basics of French in order to facilitate communication and integration into the laboratory. Experience with one or more of the following skills would be highly evaluated: protein design or the usage of artificial intelligence for structural biology, protein expression and purification, protein crystallization and macromolecular crystallography, serial crystallography, programming or scripting. Interested candidates can apply via [ https://emploi.univ-grenoble-alpes.fr/offres/doctorants/postdoctoral-resear… | https://emploi.univ-grenoble-alpes.fr/offres/doctorants/postdoctoral-resear… ] . We advice to contact Elke De Zitter ( elke.de-zitter(a)ibs.fr ) to obtain more information about the postdoctoral position and application procedure. All the best, Elke Elke De Zitter Institut de Biologie Structurale - IBS group DYNAMOP 71 avenue des Martyrs 38044 Grenoble Cedex 9, France +33 4 57 42 86 56 elke.de-zitter(a)ibs.fr

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unassigned densities
by Dmitry Semchonok 18 Dec '23

18 Dec '23

Dear colleagues, Is there a way to assign cryo-EM densities not included in the model sequence? Do you have any tools that can help? More closely, is there a way to screen the cryo-EM map + model, point out the unassigned densities, and provide the possible structures to fit in (e.g., water molecules, etc.)? Thank you. Kind regards, Dmitry

2 1

math behind beamstop_shadow_outliers
by Gao, Yunyun 13 Dec '23

13 Dec '23

Hi everyone, While I can find references for other outlier rejection options in scaling.outlier_rejction, there is none for beamstop_shadow_outliers. I am wondering what is the math behind z_lim_ac and z_lim_c. Another question would be: Does the same criteria also apply for the medium-resolution (e.g. 6-8 A) reflections? (like reflections under the beamstop support) Thanks! Best regards, Yunyun ------------------------------------ Yunyun Gao, Dr HARBOR Universitaet Hamburg Tel +49 (0)40 42838-3685

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Bug in optimize weights
by Mark Saper 08 Dec '23

08 Dec '23

I am running build 5156 on macOS 13.6.1. I am refining a multi-molecule with imperfect NCS. When I tried to use "Optimize X-ray/sterochemistry" and "Optimize X-ray/ADP weight” the program aborted with an error during the first cycle. The error was: ====================== XYZ individual (reciprocal space) ====================== AttributeError I submitted a bug report via the internal bug report system. I would appreciate how to get around this problem. Should I try the previous stable version? Many thanks, Mark _____________________ Mark A. Saper, Ph.D. Visiting Professor Dept of Microbiology and Molecular Genetics Hebrew University Faculty of Medicine Associate Professor Emeritus of Biological Chemistry University of Michigan Medical School saper(a)umich.edu <mailto:[email protected]> | +972 52 815-0480

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Reference model problem
by Luca Pellegrini 06 Dec '23

06 Dec '23

I am trying to use a reference model in real_space_refinement, but phenix stops with the message: “Cannot not restrain working model to self and a reference model simultaneously” (see below). The reference and working models are identical but bound to different ligands. As far as a I can see, all I am doing is adding the reference model in the input window and ticking the box for reference model restraints (phenix 1.21rc1-4985). Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK [cid:[email protected]]

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Error 1.21rc1-5156 macOS and cross special position
by Xavier Brazzolotto 01 Dec '23

01 Dec '23

Dear Phenix developers, I have recently updated to macOS Sonoma and updated Phenix to the latest RC (1.21rc1-5156). I do have recent data where a residue gets a bit too close to its symmetric mate. In order to be able to start the refinement, I have to select the model interpretation option « allow_polymer_cross_special_position=True » In this case, the refinement process starts and does my 3 refinement cycles. However, the UI gives me a final error message stating that I have to enable the « cross-special position » (which is already True). The refined data are present (pdb, mtz, log, cif, eff, geo) but I do not get any analysis on these data. No _info.txt, no .kin files. The log ends with a « Sorry » If I deliberately move the faulty residue a bit out of its position (no more clashing with its symmetric mate) and NOT allow the cross-special position, then the refinement ends well with the correct final data analysis. Not a big deal per se, but but I suspect a small issue in the initiation of the analysis programs (Molprobity / King / etc…). Xavier

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Re: [phenixbb] CCP4 Study Weekend 2024 - Early bird registration including standard student bursary deadline coming soon!
by Karen McIntyre - STFC UKRI 01 Dec '23

01 Dec '23

Dear all, Registration is open for the 2024 CCP4 study weekend entitled "Decision making in MX - how to be a productive structural biologist". This year we are focusing on decision-making in macromolecular crystallography: when to use what automated tool, how to interpret the output and when you need to get your hands dirty instead. The frontiers of crystallography now involve massive multi-crystal and multi-dimensional experiments. This means the more that you can leave to the automated pipelines, the more you can focus on the novel elements of your experiment. Sometimes those automated tools work, and sometimes they fail (but have maybe not told you exactly why or how). Sometimes they don't even exist. In that case, how can you return to the basics and develop new strategies to break down the barriers to publication? Once again, this year the CCP4 Study Weekend will be held as a hybrid event from the 3rd to 5th January 2024, 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 2024 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 including the ceilidh. For full details, programme, logistics and registration, please visit the Study Weekend website<https://studyweekend.ccp4.ac.uk/>. Important Key Dates: * Early bird registration final date: 19 November 2023; * Standard Student bursaries are open to all students registering during early bird period i.e. now until 19 November which cover the cost of registration plus one night accommodation; * 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). We hope to see you there! Scientific Organisers: Helen Ginn (Deutsches Elektronen-Synchrotron, DESY, Germany) Nick Pearce (Linköping University, Sweden) Clemens Vonrhein (Global Phasing Ltd, UK) Administrative Organisers: Karen McIntyre (CCP4, UK)

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The experiment is still very much needed (though AlphaFold helps a lot)
by Tom Terwilliger 01 Dec '23

01 Dec '23

Hi Structural biologist colleagues! Our article that helps you make the case that the experiment is still very much needed is now out: https://www.nature.com/articles/s41592-023-02087-4 "AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination." Nature Methods (2023) Also, here is a video on the Phenix Tutorials YouTube channel that describes this analysis: https://www.youtube.com/watch?v=ugMPYdPo8Bc (I hope you will be happy to see that you and your structural biology colleagues get the credit for making AlphaFold possible at 2:35 in the introduction of this video! Keep up the fantastic structural biology work!) All the best, Tom T -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

2 1

Possible problem with eLBOW in version 1.21rc1.5058 using smiles string
by Francisco Javier Medrano 30 Nov '23

30 Nov '23

Dear developers: I have tried to use eLBOW in version 1.21rc1.5058 to generate a cif file for a ligand and the program give me the following error: SMILES parser error:"Unable to load parsing table". The smiles string used was OP(OP(O)(O)=O)(O)=O, but it does not work for other strings. It does work if you supply a pdb file with connect records. If I use version 1.20.1-4487 with the same smiles string it does work properly. Is there any bur in the 1.21 version? Best regards -- Fº Javier Medrano Cristalografía de Macromoléculas Centro de Investigaciones Biológicas Margarita Salas C/ Ramiro de Maeztu, nº 9 Madrid - Spain

2 2

issue with restrains
by Dmitry Semchonok 22 Nov '23

22 Nov '23

Dear colleagues, The issue with the refinement (Phenix 1.21rc1-5130) The refinement does not recognize the phil parameters prepared with ReadySet. [cid:5bb12054-9715-417b-a68d-58c1228ffe56] Please prompt me on how to proceed. Thank you Kins regards, Dmitry

2 2