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PDC 2025 > PRE-Conference: Pittsburgh Diffraction Conference - registration deadline August 25,2025
by Stojanoff, Vivian 14 Aug '25

14 Aug '25

Pittsburgh Diffraction Conference You are cordially invited to attend the Pre-Conference Workshop, Crystal Clear Insights: Mastering Protein Crystallization This hands-on workshop will be held at NSLS II on October 9 prior to the Pittsburgh Diffraction Conference. “Crystal Clear Insights” aims to discuss basic and advance protein crystallization methods for advanced structural diffraction data collection. Participants will be able to select three of the five parallel hands-on sessions. To register: https://www.bnl.gov/pittsburgh-diffraction-conference/index.php If you want to register only for the workshop contact Vivian Stojanoff by email (stojanof(a)bnl.gov) and use “PDC 2025 – Crystal Clear” for your subject line. Participation is limited to 20 participants; those who wish to attend only the pre-Conference workshop will be placed on a waiting list and informed by August 26, 2025. ALL “Crystal Clear” pre-Conference PARTICIPANTS need to register until August 25, 2025, in the Brookhaven National Laboratory Guest, User and Visitor Center (GUV), as well, if you do not have a BNL Guest appointment. To register follow instructions: https://guest.bnl.gov/ If you have any question, contact: stojanof(a)bnl.gov. Tentative Program: Lecture: From Gene to Crystallization Crissy Tarver, SLAC Hand-on Topics: Vapor Diffusion Methods - from hanging drops to sitting drops Darya Marchany-Rivera, SSRL Exploring the Phase Diagram for crystals for all applications Patrick Stewart, Douglas Instruments Ltd. Nanoliter and nano/micro sized crystals using the Acoustic Droplet Ejector Alex Soares, NSLS II Microfluidics crystallization and X-ray Diffraction Sarah Perry, UMASS Amherst Sample prep for electron microscopy and X-ray diffraction TBD All topics will be offered in parallel, participants will be able to choose 3 topics and rotate through them.

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Inquiry on RMS Value in Phenix PredictAndBuild MR Output
by zx2020＠connect.hku.hk 11 Aug '25

11 Aug '25

Dear All, I hope this email finds you well. While reviewing the MR-related output files generated by Phenix PredictAndBuild (see attached screenshot), I noticed that an RMS value is set in the Phaser input section. I found that in certain cases this parameter can have a significant impact on MR results. Could you kindly advise how this RMS value is determined or calculated within Phenix PredictAndBuild? [??????] Thank you very much for your time and guidance. Best regards, Xin Zhang School of Biomedical Sciences, The University of Hong Kong

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Refine pixel size for EM map?
by Oliver Clarke 01 Aug '25

01 Aug '25

Hi, I remember asking about this some time ago, but I am not sure if it was ever implemented. Is there a way to refine just pixel size for an EM map in phenix.real_space refine (or another phenix utility)? Even just automatically rigid-body fitting a crystal structure and calculating the pixel size with max correlation would be handy. We do this at the moment using Chimera/ChimeraX, but an automated way to do it in phenix would be handy. In the absence of a crystal structure, I wonder if directly refining pixel size during real space refinement would be possible/reasonable at higher resolution (<2Å)? Cheers Oli

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Phenix LigandFit RSCC calculation questions
by Theo Teng 29 Jul '25

29 Jul '25

Dear Phenix developers, I hope this message finds you well. We had two specific questions about how the real-space correlation coefficient (RSCC) is computed when using Phenix.LigandFit: 1. What radius is used around the ligand or search center when calculating the RSCC during ligand fitting? Is this radius fixed or adaptive? 2. Which CCTBX function(s) underlie the RSCC calculation used in LigandFit? We aim to compare the placements from LigandFit to other ligand placement methods, and your response would be appreciated. Best regards, -- *Theodore W. Teng* Harvard College | Class of 2027 A.B. student in Chemical and Physical Biology Secondary in Global Health and Health Policy

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Re: phenixbb Digest, Vol 235, Issue 4 (out of office)
by Elisabeth Laurent 29 Jul '25

29 Jul '25

Thank you for your e-mail. I am out of office until August 26th, 2025. 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> 29.7.25 20:38 >>> 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. Re: Structure with high clashscore (sazanov(a)ist.ac.at) 2. Re: Structure with high clashscore (Pavel Afonine) 3. Deadline Extended: Macromolecular Crystallography - CSHL Course October 2025 (Paul Adams) 4. Phenix LigandFit RSCC calculation questions (Theo Teng) 5. Re: Phenix LigandFit RSCC calculation questions (Bernhard Rupp) ---------------------------------------------------------------------- Message: 1 Date: Tue, 22 Jul 2025 15:09:07 -0000 From: sazanov(a)ist.ac.at Subject: [phenixbb] Re: Structure with high clashscore To: phenixbb(a)phenix-online.org Message-ID: <175319694772.2856041.9789770720208691588(a)cci3.lbl.gov> Content-Type: text/plain; charset="utf-8" Hi, one more possibility - we find that if the structure is refined without hydrogens, but one or more ligands do have hydrogens (not intentionally), then Molprobity adds hydrogens to all residues and clashscore calculated by it (now including hydrogens) jumps a lot. The remedy would be to delete all hydrogens from the structure before the refinement (or refine with hydrogens added everywhere). Best Leonid JEROME JOHNSON wrote: > Hello all, > > I'm happy to join the forum! I have a problem with clashscores and would be > grateful for support. > > I have diffraction data for a 3HP-CoA Synthetase from N. maritimus resolved > to 2.7 Angstroms. For MD, I used an alphafold structure (as I understand > commonly results in high clashscore values) and after numerous rounds of > refinement, the clashscore remains high at 11. I recently tried using > gromacs to energy minimize and got values of 5 and 3 (according to > molprobity), but after refinement these values immediately jumped back up > to ~30. > > I wondered if you could describe the best way to reduce these? > > Attached is my latest round of refinement should you wish to take a look! > > Best, > Jerome ------------------------------ Message: 2 Date: Tue, 22 Jul 2025 10:29:20 -0500 From: Pavel Afonine <pafonine(a)lbl.gov> Subject: [phenixbb] Re: Structure with high clashscore To: phenixbb(a)phenix-online.org, jjohnson19(a)ku.edu.tr Message-ID: <b4b4a347-1f89-44a4-b61b-dac1d2344d24(a)lbl.gov> Content-Type: text/plain; charset=UTF-8; format=flowed Hi All, > Hi, one more possibility - we find that if the structure is refined without hydrogens, but one or more ligands do have hydrogens (not intentionally), then Molprobity adds hydrogens to all residues and clashscore calculated by it (now including hydrogens) jumps a lot. The remedy would be to delete all hydrogens from the structure before the refinement (or refine with hydrogens added everywhere). this is an interesting observation. MolProbity always adds all H to compute clashscore -- one can't compute clashscore without H present. I suspect having H on ligands only triggers it to 'think' that H are already present, and it computes clashscore without adding H to everything else. Could you please send me the file off list (the one that has H only on the ligand)? I think we better investigate this.. >> I'm happy to join the forum! I have a problem with clashscores and would be >> grateful for support. >> >> I have diffraction data for a 3HP-CoA Synthetase from N. maritimus resolved >> to 2.7 Angstroms. For MD, >> commonly results in high clashscore values) and after numerous rounds of >> refinement, the clashscore remains high at 11. 11 looks just fine. Note, clashscore=0 is not the goal because clashscore does not account for non-standard links and for example, can count as a severe clash atoms involved into nonstandard links, and similar. In Phenix Comprehensive Validation, go over the table of clashes, they are sorted, worst first, and check and try to address top few worst offenders. Pavel ------------------------------ Message: 3 Date: Tue, 22 Jul 2025 10:52:38 -0700 From: Paul Adams <pdadams(a)lbl.gov> Subject: [phenixbb] Deadline Extended: Macromolecular Crystallography - CSHL Course October 2025 To: phenixbb(a)phenix-online.org, CCP4BB(a)jiscmail.ac.uk Message-ID: <616BD923-8C42-4BFA-BCAF-4B7E60F4AC9C(a)lbl.gov> Content-Type: text/plain; charset=utf-8 Dear Colleagues, For those of you that may have missed the deadline, the application deadline has been extended to August 1st. A reminder that the Cold Spring Harbor Macromolecular Crystallography course will take place October 12-28th this year (pleased see below for more details). This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography. There are extensive lectures and practical sessions from world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation. The goal of the course is for researchers who have had some exposure to structural biology to become experts in crystallography. This is an experience in macromolecular crystallography learning that cannot be found anywhere else, and the student/teacher ratio is often 1:1. Please follow this link to the course web site: https://meetings.cshl.edu/courses.aspx?course=C-CRYS In particular, please note the information about the various fellowships, scholarships, and stipends that are available. Most applicants ultimately receive some form of financial support. If anyone has any questions please send me an e-mail, and we will be happy to answer all queries. Paul Adams -- 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 ] -- ------------------------------ Message: 4 Date: Tue, 29 Jul 2025 14:34:52 -0400 From: Theo Teng <theodoreteng(a)college.harvard.edu> Subject: [phenixbb] Phenix LigandFit RSCC calculation questions To: phenixbb(a)phenix-online.org Message-ID: <CAE39kgR2K4FxFye6YJKO9uWnwQECYhg2+AB=_vRb=NLkw9ToXA(a)mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Dear Phenix developers, I hope this message finds you well. We had two specific questions about how the real-space correlation coefficient (RSCC) is computed when using Phenix.LigandFit: 1. What radius is used around the ligand or search center when calculating the RSCC during ligand fitting? Is this radius fixed or adaptive? 2. Which CCTBX function(s) underlie the RSCC calculation used in LigandFit? We aim to compare the placements from Lig-- *Theodore W. Teng* Harvard College | Class of 2027 A.B. student in Chemical and Physical Biology Secondary in Global Health and Health Policy ------------------------------ Message: 5 Date: Tue, 29 Jul 2025 11:38:27 -0700 From: Bernhard Rupp <br(a)hofkristallamt.org> Subject: [phenixbb] Re: Phenix LigandFit RSCC calculation questions To: Theo Teng <theodoreteng(a)college.harvard.edu> Cc: phenixbb(a)phenix-online.org Message-ID: <CAA3s99dcrE3j8VRJ6cH__7jv9y1a-ve2sxWcRws3UtsKsUdmag(a)mail.gmail.com> Content-Type: text/plain; charset="UTF-8" There is a modified quote from a famous statistician, which one might keep in mind on such ventures: All ligands are wrong, but some are useful. Cheers, BR ------------------------------------------------------ Bernhard Rupp https://www.hofkristallamt.org/ br(a)hofkristallamt.org br(a)ruppweb.org +1 925 209 7429 +43 676 571 0536 ------------------------------------------------------ People can be divided into three classes: The few who make things happen; The many who watch what is happening; and the overwhelming majority who have no clue what is happening. ------------------------------------------------------ On Tue, Jul 29, 2025 at 11:35 AM Theo Teng <theodoreteng(a)college.harvard.edu> wrote: > Dear Phenix developers, > > I hope this message finds you well. > > We had two specific questions about how the real-space correlation > coefficient (RSCC) is computed when using Phenix.LigandFit: > > 1. What radius is used around the ligand or search center when calculating > the RSCC during ligand fitting? Is this radius fixed or adaptive? > > 2. Which CCTBX function(s) underlie the RSCC calculation used in LigandFit? > > We aim to compare the placements from LigandFit to other ligand placement > methods, and your response would be appreciated. > > Best regards, > -- > > *Theodore W. Teng* > Harvard College | Class of 2027 > A.B. student in Chemical and Physical Biology > Secondary in Global Health and Health Policy > _______________________________________________ > phenixbb mailing list -- phenixbb(a)phenix-online.org > To unsubscribe send an email to phenixbb-leave(a)phenix-online.org > Unsubscribe: phenixbb-leave@%(host_name)s > ------------------------------ 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 235, Issue 4 ****************************************

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Deadline Extended: Macromolecular Crystallography - CSHL Course October 2025
by Paul Adams 22 Jul '25

22 Jul '25

Dear Colleagues, For those of you that may have missed the deadline, the application deadline has been extended to August 1st. A reminder that the Cold Spring Harbor Macromolecular Crystallography course will take place October 12-28th this year (pleased see below for more details). This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography. There are extensive lectures and practical sessions from world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation. The goal of the course is for researchers who have had some exposure to structural biology to become experts in crystallography. This is an experience in macromolecular crystallography learning that cannot be found anywhere else, and the student/teacher ratio is often 1:1. Please follow this link to the course web site: https://meetings.cshl.edu/courses.aspx?course=C-CRYS In particular, please note the information about the various fellowships, scholarships, and stipends that are available. Most applicants ultimately receive some form of financial support. If anyone has any questions please send me an e-mail, and we will be happy to answer all queries. Paul Adams -- 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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Structure with high clashscore
by JEROME JOHNSON 22 Jul '25

22 Jul '25

Hello all, I'm happy to join the forum! I have a problem with clashscores and would be grateful for support. I have diffraction data for a 3HP-CoA Synthetase from N. maritimus resolved to 2.7 Angstroms. For MD, I used an alphafold structure (as I understand commonly results in high clashscore values) and after numerous rounds of refinement, the clashscore remains high at 11. I recently tried using gromacs to energy minimize and got values of 5 and 3 (according to molprobity), but after refinement these values immediately jumped back up to ~30. I wondered if you could describe the best way to reduce these? Attached is my latest round of refinement should you wish to take a look! Best, Jerome

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Syntax help: phenix.pdb_tools to remove selected bases from file
by Vorländer,Matthias Kopano 21 Jul '25

21 Jul '25

Hi everyone, I am trying to truncate an RNA chain to backbone only using phenix.pdb tools with this command: phenix.pdbtools input.cif remove="(chain IN and not (phosphate or ribose)" I get: AtomSelectionError: RuntimeError: Atom selection syntax error at word "phosphate". Atom selection string leading to error: (chain IN and not (phosphate or ribose) Based on https://phenix-online.org/documentation/reference/atom_selections.html<https://phenix-online.org/documentation/reference/atom_selections.htmlI> I thought “phosphate” and “ribose” should be valid selection key words, but can’t figure out what I am doing wrong and would appreciate your help : ) Thanks in advance and best wishes, Matthias

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smaller cell volume for accommodating protein complex & no MR solution even very similar template
by 陈成 11 Jul '25

11 Jul '25

Dear PHENIXBB people, I have been working on several data sets collected from crystals grown in co-crystallization trials containing a small molecule and Calprotectin, a heterologous protein dimer comprised of two polypeptides with around 90 and 120 amino acids respectively. The crystallographic structure of Calprotectin complexed with a 18-aa peptide have been deposited in RCSB database under PDB entry 7QUV, with cell parameters a = b = 50.8, c = 148.8 in the P 32 2 1 space group. On the contrast, the bunches of data sets I collected give cell parameters a = b = 38.3, c = 196.3 in the P 6 2 2 space group when an oscilliation angle of 0.5 degree was used or cell parameters a = b = 38.2, c = 149.0 in the P 6 2 2 space group when an oscilliation angle of 0.2 degree was used. In either cases, Matthews_coef analysis would suggest that the crystal cell cannot accommodate the whole Calprotectin complex. I had used each single protein of Calprotectin as the search template for MR, but failed as well. Though Phenix.xtriage suggest nothing wrong with the data sets, however, considering that the two polypeptide conprising Calprotectin is structurally similar, I had also tried indexing the data sets under space group spanning P2, P3 apart from P622 and then run MR by a thorough combination of each data sets and different template choices, which, in opposition to what was expected, still gave no reliable MR solution. It's noteworthy that the diffraction pattern of my crytals seemingly showed that multi-crystal problem or other intrinsic growth defects might be underconsidered. In fact, I've been encountering the above crystallographic situation for 3 times recently, which all bear the following characteristics: (1) cell volume is far smaller than expected for containing targeted macromolecules (protein/DNA) that is used for crystallization. (2) no MR solution is achieved though MR template is extremely and sometimes 100% similar. (3) growth defects such as multi-crystal or fibrous diffraction problems possibly exist. Hopefully someone may have dealt with such issues before. Any suggestions is welcomed! Sincerely Chen PS: This message is also posted on CCP4BB. Cheng Chen, Associate ProfessorSchool of Life Sciences, Building 15, Tianjin University No.92 Weijin Road, Nankai District, Tianjin 300072, China

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Re: phenixbb Digest, Vol 234, Issue 7 (out of office)
by Elisabeth Laurent 01 Jul '25

01 Jul '25

Thank you for your e-mail. I am out of office until July 8th, 2025. 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> 1.7.25 21:16 >>> 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. Re: phenix install/splash screen issue (Hekstra, Doeke Romke) 2. Data uncertainty: Minimising it and characterising the uncertainty that remains (John R Helliwell) 3. Postdoc Position - Berkeley, California (Paul Adams) ---------------------------------------------------------------------- Message: 1 Date: Sun, 15 Jun 2025 16:51:46 +0000 From: "Hekstra, Doeke Romke" <doeke_hekstra(a)harvard.edu> Subject: [phenixbb] Re: phenix install/splash screen issue To: Billy Poon <BKPoon(a)lbl.gov> Cc: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Message-ID: <BL0PR07MB38897932A0F5134154C3D9199771A(a)BL0PR07MB3889.nam prd07.prod.outlook.com> Content-Type: text/plain; charset="utf-8" Awesome. Will try later this week! -----Original Message----- From: Billy Poon <BKPoon(a)lbl.gov> Sent: Sunday, June 15, 2025 12:36 PM Cc: phenixbb(a)phenix-online.org Subject: [phenixbb] Re: phenix install/splash screen issue Hi Doeke, I got the GUI to work over VNC using ThinLinc at NERSC. The check used to work in Python 2 because comparing against None was allowed. I updated the code to skip the check if any value is None since it's not so crucial. I'll make another build available tomorrow. Let us know if you find any other issues. 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 Sat, Jun 14, 2025 at 2:51 PM Hekstra, Doeke Romke < doeke_hekstra(a)harvard.edu> wrote: > Hi Billy, > > Correct, I’m using a remote desktop (open on demand, via vnc). > > Doeke > > Get Outlook for iOS <https://aka.ms/o0ukef> > ------------------------------ > *From:* Billy Poon <BKPoon(a)lbl.gov> > *Sent:* Saturday, June 14, 2025 12:19:00 AM > *To:* Hekstra, Doeke Romke <doeke_hekstra(a)harvard.edu> > *Cc:* phenixbb(a)phenix-online.org <phenixbb(a)phenix-online.org> > *Subject:* Re: [phenixbb] phenix install/splash screen issue > > Hi Doeke, > > Are you running over X or via a virtual desktop? I just tested over X > and the GUI shows up. I'm going to try a remote desktop next. > > The issue is that the GUI is unable to calculate some limit for > placing windows. > > -- > 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 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline. > org&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=DPfbtiuJFZDsaMqRC3wABRuP0iJZMK > OIsdAAHocfxcg&m=E0acsYpZgOQ4jSQxX3QvM2W7a5egZssjBf25gnnV1q4CSsCigsm5eu > QXFzvdyEen&s=sNVrQKJJi4zo2EFXfPjtPYUxQ_hTsSQ0TT8vAPzd5Lg&e=> > > > On Sat, Jun 14, 2025 at 5:12 AM Hekstra, Doeke Romke < > doeke_hekstra(a)harvard.edu> wrote: > > Hi, > After an ostensibly error-free installation of phenix-2.0-5716 on > linux within an HPC environment, when starting the Phenix GUI, I get > the following error: > > [dhekstra@holygpu7c26105 phenix]$ phenix Error in sys.excepthook: > Traceback (most recent call last): > File > "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App > .py"> Error.show_exception_dialog(type, value, traceback) > File > "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/Err > or.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 > "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App > .py", > line 136, in OnInit > self.start_gui() > File > "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App > .py", > line 151, in start_gui > self.get_screen_params() > File > "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App > .py", > line 263, in get_screen_params > self.set_window_height(self.prefs.get_root().gui.max_dialog_height) > File > "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App > .py", > line 266, in set_window_height > if (max_height < self.screen_height) : > TypeError: '<' not supported between instances of 'NoneType' and 'int' > OnInit returned false, exiting... > > ==== > The same error occurred with phenix-2.0-5716 (both using the > Linux-x86_64 installer). > > Could you please advise? > > Thanks, > Doeke > _______________________________________________ > phenixbb mailing list -- phenixbb(a)phenix-online.org To unsubscribe > send an email to phenixbb-leave(a)phenix-online.org > Unsubscribe: phenixbb-leave@%(host_name)s > > _______________________________________________ phenixbb mailing list -- phenixbb(a)phenix-online.org To unsubscribe send an email to phenixbb-leave(a)phenix-online.org Unsubscribe: phenixbb-leave@%(host_name)s ------------------------------ Message: 2 Date: Mon, 30 Jun 2025 12:34:53 +0100 From: John R Helliwell <jrhelliwell(a)gmail.com> Subject: [phenixbb] Data uncertainty: Minimising it and characterising the uncertainty that remains To: CCP4BB(a)jiscmail.ac.uk, PHENIX user mailing list <phenixbb(a)phenix-online.org> Message-ID: <A26415F8-B11F-463A-B03F-F198BCAAA1AA(a)gmail.com> Content-Type: text/plain; charset=utf-8 Dear Colleagues, I imagine you will be interested in my post at the IUCr Committee on Data Public Forum on this topic of data uncertainty:- https://forums.iucr.org/viewtopic.php?f=39&t=6464&sid=7966a823f22e445ad1a3c… All best wishes, John -- Professor John R Helliwell DSc ------------------------------ Message: 3 Date: Tue, 1 Jul 2025 12:15:56 -0700 From: Paul Adams <pdadams(a)lbl.gov> Subject: [phenixbb] Postdoc Position - Berkeley, California To: phenixbb(a)phenix-online.org, CCP4BB(a)jiscmail.ac.uk Message-ID: <19D7DA5E-15B5-4705-A591-4F28C2F4AC9B(a)lbl.gov> Content-Type: text/plain; charset=us-ascii Dear Colleagues, We are looking for a postdoctoral candidate at Lawrence Berkeley Lab (California, US) to work on an exciting project developing computational methods for cryo-electron microscopy. You will develop mathematical approaches and computational algorithms to investigate protein conformational states from cryo-EM experiments, including single-particle imaging and cellular tomography. Goals include developing a pipeline for automated atomic modeling of heterogeneous structures from cryo-EM data using Phenix model building tools and developing methods for dealing with incomplete data and structure completion. You will work with a data analysis team for image analysis and the Phenix team for model building methods. You can start as early as August 1, 2025. Full details of the position, description of job requirements are in this link: https://jobs.lbl.gov/jobs/computational-postdoctoral-fellow-cryo-em-7131 Feel free to pass on to anyone you think might be interested. Cheers, Paul -- 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 PresidenPrincipal 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 ] -- ------------------------------ 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 234, Issue 7 ****************************************

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Postdoc Position - Berkeley, California
by Paul Adams 01 Jul '25

01 Jul '25

Dear Colleagues, We are looking for a postdoctoral candidate at Lawrence Berkeley Lab (California, US) to work on an exciting project developing computational methods for cryo-electron microscopy. You will develop mathematical approaches and computational algorithms to investigate protein conformational states from cryo-EM experiments, including single-particle imaging and cellular tomography. Goals include developing a pipeline for automated atomic modeling of heterogeneous structures from cryo-EM data using Phenix model building tools and developing methods for dealing with incomplete data and structure completion. You will work with a data analysis team for image analysis and the Phenix team for model building methods. You can start as early as August 1, 2025. Full details of the position, description of job requirements are in this link: https://jobs.lbl.gov/jobs/computational-postdoctoral-fellow-cryo-em-7131 Feel free to pass on to anyone you think might be interested. Cheers, Paul -- 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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Data uncertainty: Minimising it and characterising the uncertainty that remains
by John R Helliwell 30 Jun '25

30 Jun '25

Dear Colleagues, I imagine you will be interested in my post at the IUCr Committee on Data Public Forum on this topic of data uncertainty:- https://forums.iucr.org/viewtopic.php?f=39&t=6464&sid=7966a823f22e445ad1a3c… All best wishes, John -- Professor John R Helliwell DSc

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phenix install/splash screen issue
by Hekstra, Doeke Romke 15 Jun '25

15 Jun '25

Hi, After an ostensibly error-free installation of phenix-2.0-5716 on linux within an HPC environment, when starting the Phenix GUI, I get the following error: [dhekstra@holygpu7c26105 phenix]$ phenix Error in sys.excepthook: Traceback (most recent call last): File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 972, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/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 "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 136, in OnInit self.start_gui() File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 151, in start_gui self.get_screen_params() File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 263, in get_screen_params self.set_window_height(self.prefs.get_root().gui.max_dialog_height) File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 266, in set_window_height if (max_height < self.screen_height) : TypeError: '<' not supported between instances of 'NoneType' and 'int' OnInit returned false, exiting... ==== The same error occurred with phenix-2.0-5716 (both using the Linux-x86_64 installer). Could you please advise? Thanks, Doeke

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phenix.map_sharpening - sequence file required?
by Oliver Clarke 04 Jun '25

04 Jun '25

Hi, The new-ish map_sharpening utility seems to absolutely require a sequence file (at least on the CLI), whereas using auto_sharpen one could directly provide solvent content or estimated molecular mass. This option - molecular_mass - is still present in map_sharpening, but the program still terminates with an error - "Sorry: Need a sequence file". Is this intended? I run using the following command: phenix.map_sharpening cryosparc_P4_J199_002_volume_map.mrc resolution=2.3 molecular_mass=50000 Cheers Oli

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Reminder: Macromolecular Crystallography - CSHL Course October 2025
by Paul Adams 02 Jun '25

02 Jun '25

Dear Colleagues, A reminder that the Cold Spring Harbor Macromolecular Crystallography course will take place October 12-28th this year (pleased see below for more details). This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography. There are extensive lectures and practical sessions from world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation. The goal of the course is for researchers who have had some exposure to structural biology to become experts in crystallography. This is an experience in macromolecular crystallography learning that cannot be found anywhere else, and the student/teacher ratio is often 1:1. Please follow the link below to the course web site. In particular, please note the information about the various fellowships, scholarships, and stipends that are available. Many applicants ultimately receive some form of financial support. If anyone has any questions please send me an e-mail, and we will be happy to answer all queries. Paul Adams <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001xAZ7m1eA3JZFfHqguTfKfkZyzYIhmaBgv9…> <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001xAZ7m1eA3JZFfHqguTfKfkZyzYIhmaBgv9…> Macromolecular Crystallography <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001xAZ7m1eA3JZFfHqguTfKfkZyzYIhmaBgv9…> October 12 - 28, 2025 Applications Due: July 15 Instructors Paul Adams, Lawrence Berkeley National Laboratory Dorothee Liebschner, Lawrence Berkeley National Laboratory Janet Newman, UNSW, Australia James Pflugrath, Rigaku Americas Corporation (ret.), Texas Co-Instructor Tom Peat, UNSW, Australia Topics Basic Diffraction Theory Structure Presentation Coordinate Deposition Structure Validation Model Building and Refinement Electron Density Maps Improvement Using Predicted Models in Structure Solution and Completion Protein Structure Prediction Structure Solution by Experimental Phasing Methods (SAD, MAD, MIR, and others) and Molecular Replacement Data Collection and Processing Synchrotron X-ray Sources and Optics Crystallization (Proteins, Nucleic Acids, Complexes and Membrane Proteins) For further information and to apply please visit the Macromolecular Crystallography course website. <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001xAZ7m1eA3JZFfHqguTfKfkZyzYIhmaBgv9…> Cold Spring Harbor Laboratory - Meetings & Courses | 1 Bungtown Road | Cold Spring Harbor, NY 11724 US Unsubscribe <https://visitor.constantcontact.com/do?p=un&m=001S3f9XM7Br7nKhcnZ-APDwA%3D&…> | Update Profile <https://visitor.constantcontact.com/do?p=oo&m=001S3f9XM7Br7nKhcnZ-APDwA%3D&…> | Constant Contact Data Notice <https://www.constantcontact.com/legal/customer-contact-data-notice> -- 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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Windows 10 Retirement Date
by Billy Poon 26 May '25

26 May '25

Hi everyone, Microsoft will be dropping support for Windows 10 later this year on October 14, 2025. https://learn.microsoft.com/en-us/lifecycle/products/windows-10-home-and-pro Phenix intends to drop Windows 10 support after that date. Are there users where Windows 10 support is required after that date? 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

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Re: map-to-model FSC on low resolution map
by Pavel Afonine 26 May '25

26 May '25

Hi Jesse, there was a bug a while ago that we fixed. Are you using the latest Phenix? If not, please try it and if that does not fix the problem we'll take a closer look. All the best! Pavel On 5/26/25 08:07, bluufive2--- via phenixbb wrote: > _______________________________________________ > phenixbb mailing list -- phenixbb(a)phenix-online.org > To unsubscribe send an email to phenixbb-leave(a)phenix-online.org > Unsubscribe: phenixbb-leave@%(host_name)s

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map-to-model FSC on low resolution map
by bluufive2＠gmail.com 25 May '25

25 May '25

Hello, As part of a reviewer request for our manuscript, we are attempting to generate map-to-model FSCs for two low-resolution cryo-EM reconstructions—one at 10 Å and the other at 20 Å. We’re encountering an issue when using mtriage(both standalone and as part of the comprehensive cryo-EM validation pipeline), where the map-to-model FSC values are reported as “None”. For the 10 Å map, we were able to obtain a valid halfman-halfmap AND map-model FSC by supplying the two half-maps rather than the final unfiltered reconstruction. However, this approach has not worked for the 20 Å map, and we are still unable to retrieve a map-to-model FSC. I initially suspected the issue might be related to masking, but it appears that mtriage does not support the use of a user-provided mask. If you have any insight into what might be causing this or suggestions for alternative approaches, we would greatly appreciate your input. thanks best Jesse Hansen

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Excluding atoms from real-space refinement
by elwood.mullins＠vanderbilt.edu 14 May '25

14 May '25

Is it possible to exclude atoms in real-space refinement? Older posts seem to indicate this is, or at least was, only possible in reciprocal-space refinement. Has that changed? Using reference restraints as an alternative is less than optimal. Any help would be greatly appreciated.

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Integrative Structural Biology Summer School Padua Italy 7-11 July 2025
by Roberto Steiner 13 May '25

13 May '25

Dear All We are now at capacity for the Integrative Structural Biology Summer School www.school2025.cristallografia.org<http://www.school2025.cristallografia.org> that will be held in Padua, Italy 7-11 July 2025 However, given the interest we have decided to re-open the registration form as we have been able to secure a slightly larger room for lectures and tutorial. Registration will close this Friday at 5pm CET. With best wishes Roberto (on behalf of the organising committee) Roberto A Steiner www.steinerlab.org<http://www.steinerlab.org> https://twitter.com/steiner_lab roberto.steiner(a)kcl.ac.uk<mailto:[email protected]> Randall Centre for Cell and Molecular Biophysics Faculty of Life Sciences and Medicine King's College London Room 3.10A New Hunt's House, Guy's Campus SE1 1UL, London, UK Phone 0044 20 78488216 Fax 0044 20 78486435 roberto.steiner(a)unipd.it<mailto:[email protected]> Dipartimento di Scienze Biomediche Università degli Studi di Padova Viale G. Colombo 3 35131 Padova, Italia Telefono 0039 049 8276409 Responses to emails are not expected outside of your normal working hours.

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POSITION AVAILABLE: Visiting Research Specialist Position at the University of Illinois at Chicago
by Yury Polikanov 03 May '25

03 May '25

*Visiting Research Specialist Position Available in the Polikanov Lab <https://sites.google.com/view/polikanovlab>Department of Biological Sciences, University of Illinois at Chicago* *The Polikanov Laboratory <https://sites.google.com/view/polikanovlab> in the Department of Biological Sciences at the University of Illinois at Chicago is looking for a talented, skillful, and highly motivated researcher to fill the Visiting Research Scientist position to study the structure and function of the bacterial ribosome.* For full consideration, please submit your application along with a Cover Letter, CV, and three references by May 31, 2025. Cover letter should describe previous research accomplishments and scientific interests as well as how these fit within the scope of the research in the Polikanov lab. Questions can be addressed to Yury Polikanov at yuryp(a)uic.edu. Visiting Research Specialist- UIC Department of Biological Sciences, Polikanov Lab Hiring Department: Biological Sciences Location: Chicago, IL USA Requisition ID: 1033622 Posting Close Date: 05/31/2025 Link to Apply: https://uic.csod.com/ux/ats/careersite/1/home/requisition/14681?c=uic *Position Summary:* The Polikanov Lab is seeking a Visiting Research Specialist. Successful candidate will conduct research by using X-ray crystallography and cryo-EM techniques to obtain a structural basis for various functions of the bacterial ribosome and its inhibition by different small-molecule inhibitors. The successful candidate should have a strong theoretical background in standard biochemical, molecular biology, and biophysical methods, as well as practical skills in the most standard methods currently used in molecular biology and biochemistry (such as protein expression, purification, etc.). Knowledge in X-ray crystallography or other structural techniques is desired but not required. The successful candidate would conduct research and assist with training laboratory personnel in various techniques, experiments, and the appropriate use of research equipment. He/She would also perform data analysis and manage, document, and help with the dissemination of research activities for publication and outreach. *Duties & Responsibilities:* - Record keeping: log and track inventory of chemicals, reagents, and lab supplies - Maintain accurate records of experiments, procedures, and results - Keep the laboratory clean, organized, and free of contaminants - Glassware & Equipment Maintenance - Prepare culture media, buffers, and reagents according to protocols - Assist other researchers in the lab in conducting experiments - Purify bacterial ribosomes and all additional components necessary for the experiments, such as recombinant proteins, tRNAs - Train undergraduate and graduate students in research methods, use of equipment, record keeping, and laboratory database entry *Minimum Qualifications :* - Bachelor’s degree in biology, chemistry, biochemistry, biophysics, or related field required. Master’s degree in science preferred. - A minimum of 3 years of related research experience. - Strong background in biochemistry and molecular biology - Practical skills with the most standard methods currently used in molecular biology, and biochemistry (such as protein expression, purification) *Salary:* The budgeted salary range for the position is $48,000 to $60,000. The pay offered to the selected candidate will be determined based on factors including (but not limited to) the experience and qualifications of the selected candidate, including equivalent years in rank, training, and field or discipline; internal equity; and external market pay for comparable jobs. *About the University of Illinois Chicago* UIC is among the nation’s preeminent urban public research universities, a Carnegie RU/VH research institution, and the largest university in Chicago. UIC serves over 34,000 students, comprising one of the most diverse student bodies in the nation and is designated as a Minority Serving Institution (MSI), an Asian American and Native American Pacific Islander Serving Institution (AANAPSI) and a Hispanic Serving Institution (HSI). Through its 16 colleges, UIC produces nationally and internationally recognized multidisciplinary academic programs in concert with civic, corporate and community partners worldwide, including a full complement of health sciences colleges. By emphasizing cutting-edge and transformational research along with a commitment to the success of all students, UIC embodies the dynamic, vibrant and engaged urban university. Recent “Best Colleges” rankings published by U.S. News & World Report, found UIC climbed up in its rankings among top public schools in the nation and among all national universities. UIC has over 300,000 alumni, and is one of the largest employers in the city of Chicago. Benefits eligible positions include a comprehensive benefits package which offers: Health, Dental, Vision, Life, Disability & AD&D insurance; a defined benefit pension plan; paid leaves such as Vacation, Holiday and Sick; tuition waivers for employees and dependents. Click for a complete list of *Employee Benefits <https://www.hr.uillinois.edu/benefits/>*. *Final authorization of the position is subject to availability of funding.* *UIC is an EOE including Disability/Vets.* *The University of Illinois may conduct background checks on all job candidates upon acceptance of a contingent offer. Background checks will be performed in compliance with the Fair Credit Reporting Act* *The University of Illinois System requires candidates selected for hire to disclose any documented finding of sexual misconduct or sexual harassment and to authorize inquiries to current and former employers regarding findings of sexual misconduct or sexual harassment. For more information, visit **https://www.hr.uillinois.edu/cms/One.aspx?portalId=4292&pageId=1411899 <https://www.hr.uillinois.edu/cms/One.aspx?portalId=4292&pageId=1411899>*

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Deadline approaching: Integrative Structural Biology Summer School Padua Italy 7-11 July 2025
by Roberto Steiner 28 Apr '25

28 Apr '25

Dear All, Deadline is approaching for the International Summer School on “Current and Future Integrative Structural Biology”, taking place in the beautiful city of Padua, Italy, from 7–11 July 2025. Do not forget to register at the following link www.school2025.cristallografia.org<http://www.school2025.cristallografia.org/> This school will have a strong focus on cryo-EM, along with discussions on other cutting-edge techniques essential for modern structural biology research. Expert international speakers and tutors will provide valuable insights through lectures and practical sessions. With best wishes, Roberto (on behalf of the organising committee) Roberto A Steiner www.steinerlab.org<http://www.steinerlab.org> https://twitter.com/steiner_lab roberto.steiner(a)kcl.ac.uk<mailto:[email protected]> Randall Centre for Cell and Molecular Biophysics Faculty of Life Sciences and Medicine King's College London Room 3.10A New Hunt's House, Guy's Campus SE1 1UL, London, UK Phone 0044 20 78488216 Fax 0044 20 78486435 roberto.steiner(a)unipd.it<mailto:[email protected]> Dipartimento di Scienze Biomediche Università degli Studi di Padova Viale G. Colombo 3 35131 Padova, Italia Telefono 0039 049 8276409 Responses to emails are not expected outside of your normal working hours.

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Phenix Dock & Rebuild Python Error
by Nicholas Clark 22 Apr '25

22 Apr '25

Hi all, I'm trying to run Phenix Dock & Rebuild on a Mac (Venture 13.6.7) but I keep getting a NameError in Python that "DESKTOP_TYPE" is not defined. Does anyone have a quick way to fix this? Can I edit the code directly in that line to explicitly state that I'm on a mac or is this a variable that should be set directly in the base Python installation? Below is the entirety of the error message: NameError : global name 'DESKTOP_TYPE' is not defined Traceback (most recent call last): File "/Applications/phenix-1.20.1-4487/modules/phenix/wxGUI2/Runtime.py", line 224, in OnComplete self.handle_complete_event(event) File "/Applications/phenix-1.20.1-4487/modules/phenix/wxGUI2/Templates.py", line 491, in handle_complete_event self.add_result_panel(result) File "/Applications/phenix-1.20.1-4487/modules/phenix/wxGUI2/Templates.py", line 512, in add_result_panel params=self.params) File "/Applications/phenix-1.20.1-4487/modules/phenix/wxGUI2/Templates.py", line 980, in __init__ JobOutputPanel.__init__(self, parent) File "/Applications/phenix-1.20.1-4487/modules/phenix/wxGUI2/Windows.py", line 551, in __init__ WidgetArea.__init__(self, parent) File "/Applications/phenix-1.20.1-4487/modules/phenix/wxGUI2/Windows.py", line 512, in __init__ self.DisplayWidgets() File "/Applications/phenix-1.20.1-4487/modules/phenix/wxGUI2/Programs/DockAndRebuild.py", line 112, in DisplayWidgets if (DESKTOP_TYPE in ['mac', 'kde', 'gnome']): NameError: global name 'DESKTOP_TYPE' is not defined Thanks! Best regards, Nick Clark

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Research Specialist Position at the University of Illinois to Study Ribosome Structure | POLIKANOV Lab
by Yury Polikanov 21 Apr '25

21 Apr '25

*Research Specialist Position Available, Department of Biological Sciences, University of Illinois at Chicago - Polikanov Lab* *The Polikanov Laboratory in the Department of Biological Sciences at the University of Illinois at Chicago (IL, USA) is looking for a talented, skillful, and highly motivated researcher to fill the Research Specialist position to study the structure and function of the bacterial ribosome.* For fullest consideration, please submit an application and cover letter describing your scientific interests and how your previous research accomplishments and scientific interests fit with the scope of the research in the Polikanov research group at https://uic.csod.com/ux/ats/careersite/1/home/requisition/7573?c=uic *Position Summary:* The research in the Polikanov Laboratory at UIC is focused on understanding the basic principles of protein synthesis in bacteria, the modes of action of ribosome-targeting antibiotics, and the mechanisms of drug resistance at a structural level. This position is involved in the determination of high-resolution structures of ribosome functional complexes with various protein translation factors, tRNAs, and antibiotics using macromolecular X-ray crystallography and potentially cryo-EM techniques. Expected contributes to the design and delivery of research projects and collaborates with researchers to develop, execute, and interpret research projects. Performs complex laboratory and data collection techniques. *Duties & Responsibilities:* - Perform research relevant to the assigned projects; - Isolate, purify, and crystallize bacterial ribosomes; - Purify all additional components necessary for the crystallization experiments, such as recombinant proteins, tRNAs; - Collect X-ray diffraction data from the ribosome crystals at the APS and NSLS-II Synchrotrons; - Perform structural data analysis; - Coordinate, analyze, and document results for publication; - Directly participate in writing papers and grants based on the experimental data; - Train undergraduate and graduate students in research methods, use of equipment, record keeping, and laboratory database entry; - Attend weekly group meetings and journal club seminars. - Perform other related duties and participate in special projects as assigned. *Minimum Qualifications:* - A bachelor’s degree in chemistry, biochemistry, biophysics, or a related field is required. - A master’s degree in chemistry, biochemistry, biophysics, or a related field is preferred. - A minimum of 3 years related research experience. - Possesses and applies comprehensive knowledge of research principles, concepts, practices, and methods. - Proficient in standard molecular biology and biochemistry lab techniques, such as protein expression, and purification *Preferred Qualifications:* - Experience in structural biology (cryo-EM or X-ray crystallography); - Experience in RNA biology, ribosome, and/or protein synthesis fields. *About the University of Illinois Chicago:* UIC is among the nation’s preeminent urban public research universities, a Carnegie RU/VH research institution, and the largest university in Chicago. UIC serves over 34,000 students, comprising one of the most diverse student bodies in the nation and is designated as a Minority Serving Institution (MSI), an Asian American and Native American Pacific Islander Serving Institution (AANAPSI) and a Hispanic Serving Institution (HSI). Through its 16 colleges, UIC produces nationally and internationally recognized multidisciplinary academic programs in concert with civic, corporate and community partners worldwide, including a full complement of health sciences colleges. By emphasizing cutting-edge and transformational research along with a commitment to the success of all students, UIC embodies the dynamic, vibrant and engaged urban university. Recent “Best Colleges” rankings published by U.S. News & World Report, found UIC climbed up in its rankings among top public schools in the nation and among all national universities. UIC has nearly 260,000 alumni, and is one of the largest employers in the city of Chicago. *The University of Illinois System is an equal opportunity employer, including but not limited to disability and/or veteran status, and complies with all applicable state and federal employment mandates. Please visit Required Employment Notices and Posters <https://www.hr.uillinois.edu/cms/one.aspx?portalId=4292&pageId=5705> to view our non-discrimination statement and find additional information about required background checks, sexual harassment/misconduct disclosures, COVID-19 vaccination requirement, and employment eligibility review through E-Verify. **The university provides accommodations to applicants and employees. Request an Accommodation <https://jobs.uic.edu/request-and-accomodation/>*

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sub-unitary occupancy group restraints sum
by Kreitler, Dale 17 Apr '25

17 Apr '25

Hi, For refining an x-ray structure which has a ligand bound with multiple poses modeled as alternate confirmations, is there a way in phenix refine to maintain that the occupancy of each conformation is equal while allowing the sum total occupancy to vary (rather than equal 1)? I realize the [0,1] min/max occupancy values are adjustable parameters -- my interpretation of the docs is that this is not possible, but I thought it'd be worth asking. An example might be a ligand bound with partial occupancy near a rotational symmetry axis. Thank you, Dale ============================= Dale Kreitler AMX Beamline Scientist National Synchrotron Light Source II Building 745, Rm. 5L143 Upton, NY 11973 631-344-7318

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twinning and translational NCS issues
by Wenhui Xi 16 Apr '25

16 Apr '25

Hi all, i have this crystal which was reported severe issues with twinning and translational NCS, thus when i tried to refine its structure, the Rfree would go up to nearly 60% which making directly solving its structure very hard. i'm writing to ask are there any helpful ways to deal with this issue? Thank you! Joyce [image: image.png]

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CBMS Structural Biology Workbench - May 27 through 30, 2025 - registration deadline April 15
by Stojanoff, Vivian 14 Apr '25

14 Apr '25

Dear Colleagues, The CBMS Structural Biology Workbench will take place May 27 through 30, 2025. The first two days, May 27 and 28, are dedicated to MX and the following days May 29 and 30 to Solution Scattering and X-ray Footprintig. This is an IN-PERSON workshop. DEADLINE to REGISTER APRIL 15 https://www.bnl.gov/cbmsworkbench/ PROGRAM Macromolecular Crystallography May 27 - MX data collection on participants samples and pre-analysis May 28 - Phenix workshop "The Phenix workshop will focus on crystallographic refinement using phenix.refine. The first lecture will introduce major features and best practices of reciprocal space refinement, followed by a basic tutorial demonstrating how to run phenix.refine with default options. The second lecture will cover strategies for low-resolution refinement, including the use of secondary structure restraints and reference models. Participants who so desire will have the opportunity to work on their own data with Phenix developers available to answer questions—on phenix.refine or any other Phenix tools in the afternoon. Solution Scattering - SAXS & Xray Footprinting - XFP May 29 - Introduction to SAXS & LIX; Data collection on participants samples May 30 morning - SAXS data analysis software May 30 afternoon - Introduction to XFP and hands-on tutorial Questions can be directed to Vivian Stojanoff (stojanof(a)bnl.gov). ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?…>

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Re: phenixbb Digest, Vol 232, Issue 13 (out of office)
by Elisabeth Laurent 13 Apr '25

13 Apr '25

Thank you for your e-mail. I am out of office until April 23rd, 2025. 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> 13.4.25 20:51 >>> 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. Re: Question about geometry outliers in RealSpaceRefine (Pavel Afonine) 2. Re: DEN restraints and ECHT disorder models (Tom Burnley - STFC UKRI) ---------------------------------------------------------------------- Message: 1 Date: Fri, 11 Apr 2025 11:47:11 -0700 From: Pavel Afonine <pafonine(a)lbl.gov> Subject: [phenixbb] Re: Question about geometry outliers in RealSpaceRefine To: Kevin M Jude <kjude(a)stanford.edu>, "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Message-ID: <7968370b-7470-4fe4-aaf1-052661202ef9(a)lbl.gov> Content-Type: multipart/alternative; boundary="------------YozFq5Oyt0xmhpmEfOqMdIo0" Hi Kevin, could you please send me the file (off list)? Thanks! Pavel On 4/11/25 09:34, Kevin M Jude wrote: > > After a recent RealSpaceRefine run, the Geometry Restraints tab in the > gui reports that I have two bond angle outliers > 4 sigma, but only > lists one of them: > > D 180 MET N, D 180 MET CA, D 180 MET CB 114.170 109.342 4.2 > > So I check the logfile for the job and see: > > Bond angle restraints: 12582 > > Sorted by residual: > > angle pdb=" N MET D 180 " > > pdb=" CA MET D 180 " > > pdb=" CB MET D 180 " > > ideal model delta sigma weight residual > > 114.17 109.34 4.83 1.14e+00 7.69e-01 1.79e+01 > > angle pdb=" CA LEU B 79 " > > pdb=" CB LEU B 79 " > > pdb=" CG LEU B 79 " > > ideal model delta sigma weight residual > > 116.30 127.81 -11.51 3.50e+00 8.16e-02 1.08e+01 > > angle pdb=" C ASP B 333 " > > pdb=" N SER B 334 " > > pdb=" CA SER B 334 " > > ideal model delta sigma weight residual > > 122.74 127.19 -4.45 1.44e+00 4.82e-01 9.54e+00 > > angle pdb=" C GLN D 167 " > > pdb=" N ARG D 168 " > > pdb=" CA ARG D 168 " > > ideal model delta sigma weight residual > > 121.48 126.80 -5.32 2.04e+00 2.40e-01 6.80e+00 > > angle pdb=" C ASP B 163 " > > pdb=" N THR B 164 " > > pdb=" CA THR B 164 " > > ideal model delta sigma weight residual > > 123.47 127.30 -3.83 1.53e+00 4.27e-01 6.27e+00 > > ValidationCryoEM returns identical results except the gui says only > one > 4-sigma outlier (at //D/Met180/). PDB Validation reports only > the outlier at //B/Leu79/, which does have the largest sigma in the > above log. > > My questions are: > > 1. Why does the gui report two 4-sigma outliers but only show one? > 2. Why do the sigmas in the log file not correspond to the sigmas in > the gui? > > Best wishes > > Kevin > > -- > > Kevin Jude, PhD > > Structural Biology Research Specialist, Garcia Lab > > Howard Hughes Medical Institute > > Stanford University School of Medicine > > Beckman B177, 279 Campus Drive, Stanford CA 94305 > > > _______________________________________________ > phenixbb mailing list --phenixbb(a)phenix-online.org > To unsubscribe send an email tophenixbb-leave(a)phenix-online.org > Unsubscribe: phenixbb-leave@%(host_name)s

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DEN restraints and ECHT disorder models
by Roberto Battistutta 13 Apr '25

13 Apr '25

Dear all, From which version of Phenix are the DEN restraints and ECHT disorder models implemented in the ensemble refinement (as described in Ploscariu, N., Burnley, T., Gros, P. & Pearce, N. M. (2021). Improving sampling of crystallographic disorder in ensemble refinement. Acta Cryst. D77, 1357-1364)? Thank you very much, Roberto. Roberto Battistutta Associate Professor Department of Chemical Sciences University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistutta(a)unipd.it

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Question about geometry outliers in RealSpaceRefine
by Kevin M Jude 11 Apr '25

11 Apr '25

After a recent RealSpaceRefine run, the Geometry Restraints tab in the gui reports that I have two bond angle outliers > 4 sigma, but only lists one of them: D 180 MET N, D 180 MET CA, D 180 MET CB 114.170 109.342 4.2 So I check the logfile for the job and see: Bond angle restraints: 12582 Sorted by residual: angle pdb=" N MET D 180 " pdb=" CA MET D 180 " pdb=" CB MET D 180 " ideal model delta sigma weight residual 114.17 109.34 4.83 1.14e+00 7.69e-01 1.79e+01 angle pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " pdb=" CG LEU B 79 " ideal model delta sigma weight residual 116.30 127.81 -11.51 3.50e+00 8.16e-02 1.08e+01 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 122.74 127.19 -4.45 1.44e+00 4.82e-01 9.54e+00 angle pdb=" C GLN D 167 " pdb=" N ARG D 168 " pdb=" CA ARG D 168 " ideal model delta sigma weight residual 121.48 126.80 -5.32 2.04e+00 2.40e-01 6.80e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 123.47 127.30 -3.83 1.53e+00 4.27e-01 6.27e+00 ValidationCryoEM returns identical results except the gui says only one > 4-sigma outlier (at //D/Met180/). PDB Validation reports only the outlier at //B/Leu79/, which does have the largest sigma in the above log. My questions are: 1. Why does the gui report two 4-sigma outliers but only show one? 2. Why do the sigmas in the log file not correspond to the sigmas in the gui? Best wishes Kevin -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305

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Simulate map from model
by Ricardo Righetto 09 Apr '25

09 Apr '25

Hi, Apologies if I'm missing something obvious, but I was not able to find this in the documentation: is there a PHENIX tool for simulating Coulomb potential maps (aka "cryo-EM maps") from atomic models? I'm looking for something like the molmap <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html> command in ChimeraX, but more accurate. One such alternative is the simulate program from cisTEM, but I figured PHENIX might also have something? Thank you! -- Ricardo Diogo Righetto

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Differential density peaks and hydrophobic residues
by Lucas Souza 04 Apr '25

04 Apr '25

Hi everyone, I am refining a ~3A structure using phenix 1.21.2-5419. I am at the final stages of the refinement but I am seeing some positive density on some hydrophobic residues (mainly Ile and Leu) together with a negative density around those residues (image attached). At first, I guessed that might be related to solvent mask, so I turned on optimize_mask. That did not solve the issue, although slightly decreased R values. Diffraction data was processed with autoproc+staraniso and does not seem to be twinned (normal intensity stats + map deteriorates if twinning refinement is applied). Does anyone have a guess about that? Best, Lucas -- Lucas Souza dos Santos Laboratório de Biologia Estrutural Aplicada (LBEA) Departamento de Microbiologia Instituto de Ciências Biomédicas II - USP Cidade Universitária - São Paulo - SP CEP 05508-000

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CBMS Structural Biology Workbench - May 27 through 30, 2025 - registration deadline approaching
by Stojanoff, Vivian 03 Apr '25

03 Apr '25

Dear Colleagues, The CBMS Structural Biology Workbench will take place May 27 through 30, 2025. The first two days, May 27 and 28, are dedicated to MX and the following days May 29 and 30 to Solution Scattering and X-ray Footprintig. This is an IN-PERSON workshop. DEADLINE to REGISTER APRIL 15 https://www.bnl.gov/cbmsworkbench/ PROGRAM Macromolecular Crystallography May 27 - MX data collection on participants samples and pre-analysis May 28 - Phenix workshop "The Phenix workshop will focus on crystallographic refinement using phenix.refine. The first lecture will introduce major features and best practices of reciprocal space refinement, followed by a basic tutorial demonstrating how to run phenix.refine with default options. The second lecture will cover strategies for low-resolution refinement, including the use of secondary structure restraints and reference models. Participants who so desire will have the opportunity to work on their own data with Phenix developers available to answer questions—on phenix.refine or any other Phenix tools in the afternoon. Solution Scattering - SAXS & Xray Footprinting - XFP May 29 - Introduction to SAXS & LIX; Data collection on participants samples May 30 morning - SAXS data analysis software May 30 afternoon - Introduction to XFP and hands-on tutorial Questions can be directed to Vivian Stojanoff (stojanof(a)bnl.gov).

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for autobuild full sequence?
by James Holton 03 Apr '25

03 Apr '25

Hey all, Don't worry, nothing is funny today. I have a real question: Is there a way to force phenix.autobuild to build in the entire sequence? As in: the full length of the actual molecule that is in the crystal, such as what is supposed to go into SEQRES, regardless of "visible" density? I am trying to come up with a pipeline for prepping MD simulations of protein crystals. It seems proper to me that the molecule being simulated should be the actual molecular species, disordered bits an all. However, we don't seem to have good technology for building protein chains into "nothingness". Yes, I know Alphafold is a thing, but it is rubbish at clashes in the context of a crystal. I mean, I could write something, but does this tool already exist? Cheers, and happy Tuesday, -James Holton MAD Scientist

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CloudFlare and Spain
by Billy Poon 31 Mar '25

31 Mar '25

Hi everyone, Does anyone in Spain have issues reaching the Phenix website ( https://phenix-online.org)? Our website is behind CloudFlare and it looks like, periodically, some CloudFlare IP addresses are blocked in Spain due to some piracy issues. 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

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IBA2025 - May 5&6 2025 - Cambridge MA
by Chip Lesburg 30 Mar '25

30 Mar '25

The Industrial Biostructures America conference will take place on May 5 & 6, 2025 at the MassBioHub in Cambridge MA. The conference was launched in 2018 to bring the industry-based structural biology community together for two days of presentations and networking. This is a great place for industrial structural biologists, as well as those who are industry-curious. The conference will feature keynote presentations by: * Dr. Stephen K. Burley, Director RCSB Protein Data Bank and Rutgers University Professor * Dr. James Fraser, Professor and Chair Department of Bioengineering and Therapeutics Sciences at UCSF * Dr. Stephen Harrison, Professor Harvard Medical School/Investigator Howard Hughes Medical Institute * Dr. Mark Murcko, Founding CSO/Board Member at Dewpoint Therapeutics and Relay Therapeutics Conference information is available at https://industrialbiostructuresamerica.org along with guidelines for submitting abstracts for scientific presentations during the conference. Scientific sessions will cover the following topics: * Structural Biology of Targeted Protein Degradation: Glues, TCs & DUBs * Developing Fragments to Drugs: Challenges & Victories * Molecular Dynamics and Allostery - Bridging Experimental and Computational Drug Discovery * Membrane Protein Structure Guided Design * CryoEM Synergies with Molecular Modeling and Computational Models * Biologics (Antibody Design & ADCs) * AI/ML in Structural Biology and Drug Discovery * Hot Topics (SBDD, Kinases, RNA) The abstract deadline is April 1. Space is limited so if you're interested, please register soon. Contact us at iba(a)proteros.com<mailto:[email protected]> for information regarding Exhibitor and Sponsor opportunities [cid:logo_c70edd4a-e7f0-4d54-be6f-d03f53f0c961.png] Charles Lesburg Vice President, Structural Biology odysseytx.com<https://protect.checkpoint.com/v2/___https:/odysseytx.com/___.YzJ1Om9keXNzZ…> This message is for the named person's use only. It may contain confidential, proprietary or legally privileged information. If you receive this message in error, please immediately delete it and all copies of it from your system, destroy any hard copies of it and notify the sender. ODYSSEY THERAPEUTICS, INC. ("ODYSSEY THERAPEUTICS") reserves the right to monitor all e-mail communications through its networks. ODYSSEY THERAPEUTICS cannot be committed by this e-mail or warrant the accuracy or validity of any information presented. Any views expressed in this message are those of the individual sender.

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can not launch phenix gui
by lzhlizehou＠outlook.com 29 Mar '25

29 Mar '25

Dears, I am using Ubuntu 24.04 and have successfully installed phenix-1.21.2-5419. However, when I attempt to launch the GUI by running the phenix command, it fails with the following error: Error in sys.excepthook: Traceback (most recent call last): File "/usr/local/phenix-1.21.2-5419/modules/phenix/wxGUI2/App.py", line 961, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/usr/local/phenix-1.21.2-5419/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 "/usr/local/phenix-1.21.2-5419/build/../modules/phenix/wxGUI2/command_line/main.py", line 34, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.21.2-5419/build/../modules/phenix/wxGUI2/command_line/main.py", line 28, in run wxapp = App.PhenixApp(args) File "/usr/local/phenix-1.21.2-5419/modules/phenix/wxGUI2/App.py", line 84, in __init__ wx.App.__init__(self, 0) File "/usr/local/phenix-1.21.2-5419/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8628, in __init__ self._BootstrapApp() File "/usr/local/phenix-1.21.2-5419/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 "/usr/local/phenix-1.21.2-5419/modules/phenix/wxGUI2/App.py", line 118, in OnInit show_splash_screen(timeout=2000) File "/usr/local/phenix-1.21.2-5419/modules/phenix/wxGUI2/App.py", line 1015, in show_splash_screen dlg,-1,citations.format_citation(citations.citations_db.get("phenix"))) File "/usr/local/phenix-1.21.2-5419/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) Could you kindly advise on how to resolve this issue? I would greatly appreciate your assistance. Looking forward to your reply. Best regards Li

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Call for Abstracts - Combining experimental data with predicted models - Session at the ACA Meeting, July 18-23, 2025
by Christopher Williams 24 Mar '25

24 Mar '25

Dear All, Rakhi Rajan and I are co-chairing the session "Combining experimental data with predicted models for structure determination" session at the 75th American Crystallographic Association Meeting in Lombard, IL (near Chicago) from July 18–23, 2025. It's a great meeting, and we encourage both general attendance and submissions for our session. We welcome abstract submissions for both talks and posters. If you're interested, please submit your abstract at https://www.acameeting2025.com/. Deadlines are fast approaching: March 31 – Deadline for oral abstracts & travel grant applications April 30 – Deadline for poster abstracts We invite contributions of novel methods and pipelines for combining prediction and experiment. We also invite stories of working with predictions and data. Have you gotten into the weeds with AlphaFold? Has structure prediction let you better design an experiment? Or has experimental data revealed an important detail missing from prediction? We want to hear about it! If you're interested in sponsoring our session, please reach out as well. -Christopher Williams ---Richardson Lab, Duke University -Rakhi Rajan ---University of Oklahoma

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Issues with zero B-factor and ADP refinement
by sylee00＠snu.ac.kr 23 Mar '25

23 Mar '25

Dear all, I am encountering issues related to B-factors and ADP refinement in Phenix and would appreciate any insights or suggestions. I am currently working on my first PDB file, but I've noticed that many atoms in the PDB file have a B-factor of 0. As far as I understand, B-factor values are calculated by ADP refinement in Phenix real-space refinement, but even after running real-space refinement (with ADP on in refinement settings), the B-factor remains 0 for many atoms. I am currently using Phenix 1.20 on Windows (Newest version available on window). I also attempted to run Phenix 1.21 on a Linux in other computer, but when ADP refinement is enabled, the process starts normally but halts during the ADP refinement step. So I couldn't test whether the issue is fixed in the newest version. Aside from the B-factor issue, I am also experiencing an inssue related to ADP refinement: When I run real-space refinement with ADP refinement enabled, the process starts normally but halts during the ADP refinement step. According to the log file, other refinement steps proceed without issues, but it fails to progress at the ADP refinement stage. Additionally, when I try to pause the process, I receive a "NoSuchProcess" error, so ADP refinement process may have unexpectedly terminated. At first, I thought it's the issue related to system performance or hardware differences, because adp refinement with this pdb file and identical parameters works on some computer but fails on others (the same version of Phenix). Still it's weird because this issue has occurred unexpectedly, as ADP refinement previously worked in my computer under the same conditions without any problems and also other PDB files run without any problems in my computer. I would appreciate any insights or suggestions on how to resolve this. Thanks

3 3

phenix low resolution refinement strategies
by a131943017＠163.com 20 Mar '25

20 Mar '25

Hi, how do I set the optimization parameters to make free R lower for 3.2Å x-ray crystallography data, or in other words, how do I go about determining whether the optimization strategy is appropriate or not? Questions from a Phenix Beginner.

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seeking help for phenix - coot model building
by tim smith 20 Mar '25

20 Mar '25

Hi everyone, I’m currently working on building a model and have encountered some difficulties with the map-model process. I would greatly appreciate it if anyone could assist me in either helping to build the model or teaching me how to do it. I’m happy to offer a suitable reward for your time and help. Thank you in advance for considering! Regards, Stim

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CSD changes conformation to planar during phenix.refine
by Andrea Smith 20 Mar '25

20 Mar '25

Hi all, I have a structure where I clearly see that one of the cysteines is oxidised. I have modelled CSD instead of CYS and when I do real space refine in Coot, the CSD sits nicely in the density. When I submit the phenix.refine job, I can see that the geometry changes and now the SOOH is planar. I tried to add the CSD.cif from PDB into phenix.refine as restraints, but it doesn't help and during the automatic refinement the geometry is changed to planar again. Anyone experienced same thing? What do I do? Thank you, Andrea

2 1

Trouble with GTP/GDP refinement.
by DIEGO ORTIZ DE ELGUEA LOPEZ DE DICASTILLO 18 Mar '25

18 Mar '25

Dear phenixbb: I'm working with a GTP binding protein and have had some problems running phenix_refine. In my unit cell there are two molecules one with GDP and one with GTP, which I added in Coot(0.9.8). When refining the following error message pops-up : "Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols:4 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modifications and apply_cif_link parameter definitions if necessary". Checking the log file I found that the problem seems to be hydrogen atoms from these ligands Number of atoms with unknown nonbonded energy type symbols: 4 "HETATM 6499 H5' GTP A 501 .*. H " "HETATM 6502 H5'' GTP A 501 .*. H " "HETATM12939 H5' GDP B 501 .*. H " "HETATM12940 H5'' GDP B 501 .*. H " Including the corresponding .CIF files (dowloaded from PDB) did not solve the problem and the same error popped. Since I'm in the initial stages of the refinement I'm running phenix with bindividuals. Could anybody save my day giving me some light into this issue? Cheers, Diego

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.cif file has 'UNK' auth_asym_id
by Kevin M Jude 14 Mar '25

14 Mar '25

I’ve finished refining a structure with three protein chains A, B, C. The pdb file looks ‘normal’ to me, but when I inspect the .cif file written by phenix, the auth_asym_id for chains B and C is ‘UNK’. label_asym_id is correct for all chains. I’m not really sure what the difference is between the auth_ and label_ fields. When I try to perform actions on the .cif file, I get duplicate atom label errors. Here’s a few example lines from the .pdb and .cif files, where auth_asym_id is field 6 and label_asym_id is field 16 ATOM 460 OXT PRO A 59 5.272 55.689 31.481 1.00 52.63 O ANISOU 460 OXT PRO A 59 6541 6212 7244 1448 1260 96 O TER ATOM 461 N ALA B 2 39.292 61.974 39.403 1.00 67.81 N ANISOU 461 N ALA B 2 7118 8729 9916 -1711 -388 2066 N ATOM 460 OXT . PRO A 59 ? 5.27169 55.68852 31.48123 1.000 52.63052 O ? A ? 58 1 ATOM 461 N . ALA UNK 2 ? 39.29207 61.97430 39.40271 1.000 67.80544 N ? B ? 1 1 I’m able to convert the pdb file to a usable cif file using gemmi but wanted to report this weird behavior with phenix 1.21.2_5419. -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305

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Pdb validation report via phenix
by Stachowski, Tim 12 Mar '25

12 Mar '25

I’ve always found the phenix.get_pdb_validation tool to be super helpful to gauge where my refinements are relative to the PDB, especially since I work mainly through the command line. But sometime around late last year, the R-free metric stopped being calculated (probably related to “EDS: FAILED”). Is there a way to bring this part of the tool back – or does anyone have a work around they can share? I’m running the command like: phenix.get_pdb_validation_report final-coot-3_refine_001.reflections.cif final-coot-3_refine_001.cif with version: phenix-2.0rc1-5599 Thanks Tim -- Tim Stachowski, PhD St. Jude Children’s Research Hospital ________________________________ Email Disclaimer: www.stjude.org/emaildisclaimer Consultation Disclaimer: www.stjude.org/consultationdisclaimer

2 1

Refining the structure of Ribosome and the system crash
by Rajnandani Kashyap 12 Mar '25

12 Mar '25

Hello Everyone I am trying to run jobs in phenix (real space refinement alignment with the other modelling jobs), but the system always crashes, and refinement doesn't complete. This is the structure of ribosome, and I am wondering what to do to get through the refinement. Is there any specific parameters I should be using. I tried to change the processors to 15 for a 20-processor computer. Let me know. Thanks in advance. FYI: There is no error message in the log. Best, Rajnandani ---------------------------------------------------------------------- Rajnandani Kashyap, Ph.D. Postdoctoral Fellow Department of Biochemistry and Molecular Biology Saint Louis University, Antony Lab 1205 Carr Lane, DRC 451 St. Louis, MO 63104 https://orcid.org/0000-0002-9141-1168 -----------------------------------------------------------------------

1 0

Ion placement (anomalous) + occupancy refinement
by miha.pavsic＠fkkt.uni-lj.si 06 Mar '25

06 Mar '25

Hi everyone, I have a dataset from a protein that contains 2 Ca2+ binding sites. The Ca2+ loaded protein was crystallized in the presence of Tb3+ which at one site mostly replaced Ca2+, however at the other site the Tb3+/Ca2+ ratio appears to be much lower (judging from anomalous map; data collected at 1.3 Å wavelength, MR for phasing). The occupancy sum of Tb3+ and Ca2+ at each of the two sites is strongly believed to be 1. While I am aware of the ion placement option in phenix.refine, I am not so sure how to refine the partial occupancies using anomalous data, if possible. Many thanks for any hints, Miha

3 2

AKM in Phenix
by lucas.santosouza＠outlook.com 06 Mar '25

06 Mar '25

Hi everyone, Is there still support for the generation of Average Kick Maps in Phenix? I am using both versions 1.21.2-5419 and the nightly build 2.0rc1-5555. I added kicked=True to the maps.params, but phenix.maps gives me "Unused parameter definitions: maps.map_coefficients.kicked (file "maps.params", line 53)". I also cannot see the "Kicked map" check box in the Create Maps GUI. Cheers, Lucas

2 1

Refine partially occupied ligand in active site containing chloride ions
by Stephen.carr＠rc-harwell.ac.uk 06 Mar '25

06 Mar '25

Dear phenix bb, I am trying to refine a ligand in the active site of my protein where the ligand occupancy is ~50%. The empty active site contains two chloride ions and the residual density from these ions is very prominent when the model is refined with the ligand alone. I would like to refine the model with both the ligand and chloride ions present and have been trying to do this with altLoc flags but so far with no luck. I'm assuming that since the Cl ions more-or-less directly overlay atoms from the ligand positional refinement keeps pushing them out of the density. I'm sure there is a simple way to get around this and I would be grateful for any suggestions. Best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.carr(a)rc-harwell.ac.uk tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.

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Program crash
by F.Xavier Gomis-Rüth 05 Mar '25

05 Mar '25

Dear all, I recently upgraded my MacOS to Sequoia 15.3.1 and found that previous phenix jobs that ran without problem suddenly crashed with the installation (phenix-1-21.2-5419) I had since August 2024. So I installed the latest on-built (phenix-2.0rc-5617) but it nonetheless crashed with the message below. Any help would be greatly appreciated. Best, Xavier XGRMAC:cyc3 > Could not import the compiled Python-sander interface.Traceback (most recent call last): File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 8, in <module> run_program(real_space_refine.Program) File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/iotbx/cli_parser.py", line 980, in run_program task.run() File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1524, in energies_sites pair_proxies = self.pair_proxies( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.7151 > 50: distance: 0 - 1: 15.382 distance: 1 - 2: 14.133 distance: 1 - 3: 15.077 distance: 4 - 5: 11.010 distance: 5 - 6: 5.064 distance: 5 - 8: 12.166 distance: 6 - 7: 9.252 distance: 6 - 15: 4.656 distance: 8 - 9: 6.568 distance: 9 - 10: 41.112 distance: 9 - 11: 19.959 distance: 10 - 12: 4.365 distance: 11 - 13: 12.611 distance: 12 - 14: 28.654 distance: 13 - 14: 25.314 distance: 15 - 16: 7.291 distance: 16 - 17: 12.341 distance: 16 - 19: 4.354 distance: 17 - 18: 11.820 distance: 17 - 26: 9.661 distance: 19 - 20: 7.438 distance: 20 - 21: 17.074 distance: 20 - 22: 19.126 distance: 21 - 23: 7.637 distance: 22 - 24: 3.434 distance: 23 - 25: 24.169 distance: 24 - 25: 8.875 distance: 26 - 27: 10.037 distance: 27 - 28: 9.377 distance: 27 - 30: 12.844 distance: 28 - 29: 12.437 distance: 28 - 34: 22.926 distance: 30 - 31: 46.409 distance: 31 - 32: 6.849 distance: 31 - 33: 21.459 distance: 34 - 35: 12.375 distance: 34 - 40: 15.635 distance: 35 - 36: 10.511 distance: 35 - 38: 12.461 distance: 36 - 37: 11.525 distance: 36 - 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77: 13.841 distance: 76 - 78: 23.906 distance: 77 - 79: 27.669 distance: 78 - 80: 29.196 distance: 79 - 80: 27.009 --

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