[phenixbb] Re: phenixbb Digest, Vol 234, Issue 7 (out of office)

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: [email protected] Thank you for your understanding. With kind regards, Elisabeth Laurent

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1.7.25 21:16 >>>

Send phenixbb mailing list submissions to [email protected] To subscribe or unsubscribe via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] 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" Subject: [phenixbb] Re: phenix install/splash screen issue To: Billy Poon Cc: "[email protected]" Message-ID: Content-Type: text/plain; charset="utf-8" Awesome. Will try later this week! -----Original Message----- From: Billy Poon Sent: Sunday, June 15, 2025 12:36 PM Cc: [email protected] 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 < [email protected]> 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 *Sent:* Saturday, June 14, 2025 12:19:00 AM *To:* Hekstra, Doeke Romke *Cc:* [email protected] *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 < [email protected]> 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 -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

_______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s ------------------------------ Message: 2 Date: Mon, 30 Jun 2025 12:34:53 +0100 From: John R Helliwell Subject: [phenixbb] Data uncertainty: Minimising it and characterising the uncertainty that remains To: [email protected], PHENIX user mailing list Message-ID: 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=7966a823f22e445ad1a3ce5f9c42cdca All best wishes, John -- Professor John R Helliwell DSc ------------------------------ Message: 3 Date: Tue, 1 Jul 2025 12:15:56 -0700 From: Paul Adams Subject: [phenixbb] Postdoc Position - Berkeley, California To: [email protected], [email protected] Message-ID: <[email protected]> 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 [ [email protected] ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ [email protected] ][ 1-510-486-5455 ] -- ------------------------------ Subject: Digest Footer _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] ------------------------------ End of phenixbb Digest, Vol 234, Issue 7 ****************************************