July 2025 - phenixbb - phenix-online.org

Syntax help: phenix.pdb_tools to remove selected bases from file
by Vorländer,Matthias Kopano 18 Jul '25

18 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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