April 2025 - phenixbb - phenix-online.org

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 10 Apr '25

10 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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