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PDB deposition question: processed data in P6₃22, refined model in P6₃
by fbetulertem＠gmail.com 06 Jul '26

06 Jul '26

Hello everyone,   I have a question regarding PDB deposition.   The processed diffraction data are in P6₃22, while the refined structure is in P6₃. During PDB deposition, the validation server reports a completeness of only ~51% which appears to result from the difference in symmetry between the processed data and the refined model.   Would it be acceptable to deposit the structure in this situation, or should the diffraction data be reprocessed in P6₃ and refined again before deposition?   Thank you very much for your advice! Best, Betul

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Re: phenixbb Digest, Vol 246, Issue 21 (out of office)
by Elisabeth Laurent 26 Jun '26

26 Jun '26

Thank you for your email. I am currently out of the office until July 1, 2026. I will respond to your email as soon as possible upon my return. For urgent matters, please contact: bmca(a)boku.ac.at Thank you for your understanding. Kind regards, Elisabeth Laurent >>> <phenixbb-request(a)phenix-online.org> 26.6.26 23:41 >>> Send phenixbb mailing list submissions to phenixbb(a)phenix-online.org To subscribe or unsubscribe 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. CBMS Lecture Series - Chakraborty - 24 June 2026 (Stojanoff, Vivian) 2. DECTRIS assumes stewardship of XDS (Kay Diederichs) 3. Cryo-EM staff scientist opportunity in Madison, WI (Eric Montemayor) ---------------------------------------------------------------------- Message: 1 Date: Thu, 18 Jun 2026 23:54:22 +0000 From: "Stojanoff, Vivian" <stojanof(a)bnl.gov> Subject: [phenixbb] CBMS Lecture Series - Chakraborty - 24 June 2026 To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Cc: "Stojanoff, Vivian" <stojanof(a)bnl.gov> Message-ID: <DM6PR09MB53509CC4CDC4BD3359082AA9CEE32(a)DM6PR09MB5350.nam prd09.prod.outlook.com> Content-Type: text/plain; charset="utf-8" You are cordially invited to join the Center for Biomolecular Structure Lecture Series ……….. Saumen Chakraborty The University of Mississippi WEDNESDAY, June 24, 13:30 (EDT) "Artificial Metalloproteins to Harvest Solar Energy and Small Molecule Activation" Register in advance for this meeting: https://bnl.zoomgov.com/j/1608968233?pwd=zJn5FYvcPM58P1CfantsS6bhTiMIIW.1 Time conversion Link: https://www.worldtimebuddy.com/<https://urldefense.com/v3/__https:/gcc02.safelinks.protection.outlook.com/?…> Abstract: Metalloenzymes catalyze complex reactions with unprecedented efficiency. These enzymes are promising candidates for various biotechnological applications, including producing alternative fuels and pharmaceuticals. Oftentimes, the innate complexity of these metalloenzymes prohibits a true appreciation of their full capability and a detailed understanding of their structure-function relationships. One approach to alleviating this issue is to design artificial metalloenzymes (ArMs) that still contain the metal of interest in a biomolecular environment, allowing the chemistry to be performed in aqueous media. The protein scaffold prevents unwanted side reactions. In addition, the protein environment allows one to alter outer sphere interactions to fine-tune their reorganization energies and reactivity. In this seminar, I will present two complementary approaches to designing Ni and Cu-containing ArMs – artificial hydrogenases and artificial C-H peroxidation catalysts utilizing protein reengineering and de novo protein design approaches. ------------------------------ Message: 2 Date: Tue, 23 Jun 2026 08:24:37 -0000 From: "Kay Diederichs" <kay.diederichs(a)uni-konstanz.de> Subject: [phenixbb] DECTRIS assumes stewardship of XDS To: phenixbb(a)phenix-online.org Message-ID: <178220307724.3620199.8539268109861560581(a)cci3.lbl.gov> Content-Type: text/plain; charset="utf-8" DECTRIS, a major manufacturer of X-ray and electron detectors, has assumed official stewardship of XDS. As most readers of this mailing list used globally in macromolecular crystallography to process raw diffraction data. The software plays a critical role in helping structural biologists determine the 3D structures of complex biomolecules. By taking over its management, DECTRIS guarantees the long-term maintenance, stability, and compatibility of this scientific tool. A primary goal of the corporate stewardship is to ensure long-term availability, and scientific reproducibility of results. DECTRIS has committed to keeping XDS completely free of charge for academic and non-profit research use. DECTRIS is removing the 12-month expiration constraint that previously forced academics to update their software. There will be a single version of XDS for both academic and proprietary use, which will be publicly downloadable upon registration. Academic users will enjoy unlimited free use. Furthermore, academic labs and beamlines that process data on behalf of commercial customers holding a valid XDS license will not need to purchase a separate license themselves. The company's backing transitions a historically single-developer academic codebase into a secured, corporate-supported framework. However, Wolfgang Kabsch and I keep working on XDS. For more information, please read the official press release at https://dectris.com/en/company/news/newsroom/news/dectris-assumes-stewardsh… Kay Diederichs ------------------------------ Message: 3 Date: Fri, 26 Jun 2026 16:40:29 -0500 From: Eric Montemayor <montemayor.eric(a)gmail.com> Subject: [phenixbb] Cryo-EM staff scientist opportunity in Madison, WI To: phenixbb(a)phenix-online.org Message-ID: <CAL4G_aJMuc6JWwQHHBTL3BoVbSx75HgObedUWZ7b3ATwuizn3Q(a)mail.gmail.com> Content-Type: text/plain; charset="UTF-8" See below if you’re interested in driving cutting-edge science and technology development at the interface of academia and industry! --------------------------------------------------- UW-Madison’s Department of Biochemistry currently has a full-time opening for a Cryo-EM Scientist in the Cryo-EM Research Center (CEMRC) and NIH-supported Midwest Center for Cryo-Electron Tomography (MCCET). These centers house state-of-the-art instrumentation and computational infrastructure, including multiple 300 keV and 200 keV TEMs, cryo-FIB-SEMs, along with conventional and high-pressure vitrification equipment. The centers provide hands-on training for all new staff so they are subsequently empowered to train and support users across the entire experimental and computational cryo-EM/ET workflow. The centers also provide their staff with opportunities for co-authoring publications, presenting at conferences, obtaining grant-writing experience, along with gaining experience in user-facing scientific support. Additional details linked below. Informal inquiries may be sent to cryoem(a)biochem.wisc.edu https://jobs.wisc.edu/jobs/cryo-em-scientist-madison-wisconsin-united-states https://cryoem.wisc.edu/ https://www.cryoetportal.org Regards, Eric J. Montemayor, PhD. ------------------------------ Subject: Digest Footer _______________________________________________ phenixbb mailing list -- phenixbb(a)phenix-online.org To unsubscribe send an email to phenixbb-leave(a)phenix-online.org ------------------------------ End of phenixbb Digest, Vol 246, Issue 21 *****************************************

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Cryo-EM staff scientist opportunity in Madison, WI
by Eric Montemayor 26 Jun '26

26 Jun '26

See below if you’re interested in driving cutting-edge science and technology development at the interface of academia and industry! --------------------------------------------------- UW-Madison’s Department of Biochemistry currently has a full-time opening for a Cryo-EM Scientist in the Cryo-EM Research Center (CEMRC) and NIH-supported Midwest Center for Cryo-Electron Tomography (MCCET). These centers house state-of-the-art instrumentation and computational infrastructure, including multiple 300 keV and 200 keV TEMs, cryo-FIB-SEMs, along with conventional and high-pressure vitrification equipment. The centers provide hands-on training for all new staff so they are subsequently empowered to train and support users across the entire experimental and computational cryo-EM/ET workflow. The centers also provide their staff with opportunities for co-authoring publications, presenting at conferences, obtaining grant-writing experience, along with gaining experience in user-facing scientific support. Additional details linked below. Informal inquiries may be sent to cryoem(a)biochem.wisc.edu https://jobs.wisc.edu/jobs/cryo-em-scientist-madison-wisconsin-united-states https://cryoem.wisc.edu/ https://www.cryoetportal.org Regards, Eric J. Montemayor, PhD.

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DECTRIS assumes stewardship of XDS
by Kay Diederichs 23 Jun '26

23 Jun '26

DECTRIS, a major manufacturer of X-ray and electron detectors, has assumed official stewardship of XDS. As most readers of this mailing list know, XDS is a software package used globally in macromolecular crystallography to process raw diffraction data. The software plays a critical role in helping structural biologists determine the 3D structures of complex biomolecules. By taking over its management, DECTRIS guarantees the long-term maintenance, stability, and compatibility of this scientific tool. A primary goal of the corporate stewardship is to ensure long-term availability, and scientific reproducibility of results. DECTRIS has committed to keeping XDS completely free of charge for academic and non-profit research use. DECTRIS is removing the 12-month expiration constraint that previously forced academics to update their software. There will be a single version of XDS for both academic and proprietary use, which will be publicly downloadable upon registration. Academic users will enjoy unlimited free use. Furthermore, academic labs and beamlines that process data on behalf of commercial customers holding a valid XDS license will not need to purchase a separate license themselves. The company's backing transitions a historically single-developer academic codebase into a secured, corporate-supported framework. However, Wolfgang Kabsch and I keep working on XDS. For more information, please read the official press release at https://dectris.com/en/company/news/newsroom/news/dectris-assumes-stewardsh… Kay Diederichs

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CBMS Lecture Series - Chakraborty - 24 June 2026
by Stojanoff, Vivian 18 Jun '26

18 Jun '26

You are cordially invited to join the Center for Biomolecular Structure Lecture Series ……….. Saumen Chakraborty The University of Mississippi WEDNESDAY, June 24, 13:30 (EDT) "Artificial Metalloproteins to Harvest Solar Energy and Small Molecule Activation" Register in advance for this meeting: https://bnl.zoomgov.com/j/1608968233?pwd=zJn5FYvcPM58P1CfantsS6bhTiMIIW.1 Time conversion Link: https://www.worldtimebuddy.com/<https://urldefense.com/v3/__https:/gcc02.safelinks.protection.outlook.com/?…> Abstract: Metalloenzymes catalyze complex reactions with unprecedented efficiency. These enzymes are promising candidates for various biotechnological applications, including producing alternative fuels and pharmaceuticals. Oftentimes, the innate complexity of these metalloenzymes prohibits a true appreciation of their full capability and a detailed understanding of their structure-function relationships. One approach to alleviating this issue is to design artificial metalloenzymes (ArMs) that still contain the metal of interest in a biomolecular environment, allowing the chemistry to be performed in aqueous media. The protein scaffold prevents unwanted side reactions. In addition, the protein environment allows one to alter outer sphere interactions to fine-tune their reorganization energies and reactivity. In this seminar, I will present two complementary approaches to designing Ni and Cu-containing ArMs – artificial hydrogenases and artificial C-H peroxidation catalysts utilizing protein reengineering and de novo protein design approaches.

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Creating a bond between symmetry mates on phenix
by Ezennubia, Purity 12 Jun '26

12 Jun '26

Hello everyone, I am new to this forum and I am glad this exists for discussions between phenix users. I have been trying to create a bond between two atoms belonging to different symmetry but when I create the bond restraints on phenix, I get an error message that says custom bonds with excessive length and I later realized the problem is not the bond length but the fact that the two atoms are in different symmetry. Is there a way to make this work on phenix? I would love suggestions on this. Thank you, Purity

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comprehensive validation (cryoem)
by Roberto Marabini 11 Jun '26

11 Jun '26

Hi, We are using the Phenix protocol "Comprehensive Validation (CryoEM)" (version 2.0.5936). The input structure file is provided in mmCIF format. We have observed that the protocol fails when chain IDs contain three characters, whereas it completes successfully when chain IDs contain two characters. Based on this behavior, we suspect that the protocol may internally convert the input mmCIF file to the legacy PDB format. Could you please confirm whether this assumption is correct? If such a conversion is performed internally, we would also like to understand how the protocol handles structures that exceed the limitations of the PDB format, for example files containing more than 99,999 atoms or chain identifiers that are not supported by the traditional PDB specification. When the protocol fails the following warnings are reported: Bad HELIX record, was skipped: HELIX 1 1 MET0Ah 7 HIS0Ah 14 1 8 Bad HELIX record, was skipped: HELIX 2 2 SER0Ah 25 GLU0Ah 36 1 12 ... Bad sense in SHEET record: '9' Thank you for your help. Best regards, Roberto

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GUI installer for Phenix crashes after 15 minutes
by Mark Saper 08 Jun '26

08 Jun '26

I have an Intel MacBook Pro running macOS 15.7.7. I downloaded the appropriate GUI installer for Phenix 2.1. The installation runs for about 15 min and then fails with a vague message. This happened to me previously with Phenix 2.0. I used the command line installer in each case and that was successful. I reported the problem but I received no response. Can the GUI installers be fixed? 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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new BUILT of XDS
by kay.diederichs＠uni-konstanz.de 06 Jun '26

06 Jun '26

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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real space refine ADPs
by Leonid Sazanov 06 Jun '26

06 Jun '26

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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