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phenix.model_idealization
by Manoj saxena 20 Jun '23

20 Jun '23

Hi , I am trying to fix a pdb file that was obtained from Rosetta and has some distorted helices so I trier to fix that with > phenix.model_idealization model.pdb use_ss_restraints = True I am attaching the log file , here is the end of the log file. Any suggestions on what's going on ? " NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Traceback (most recent call last): File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 1118, in <module> run(sys.argv[1:]) File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 1106, in run mi_object.run() File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 548, in run self._setup_model_h() File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 478, in _setup_model_h params_h.pdb_interpretation = self.model._pdb_interpretation_params.pdb_interpretation AttributeError: 'NoneType' object has no attribute 'pdb_interpretation'" My aim is to idealize the secondary structure. I first tried it in Isolde but the EM density is not great and always leads to some distortion. So I was wondering if I can do this fix in Phenix. Is this model idealization tool the best approach? or I have to go in and fix things manually. Thanks Manoj

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Glycosidic bonds in cif
by Engin Özkan 18 Jun '23

18 Jun '23

Hi, I am trying to deposit cif files from phenix.refine using the last stable version and the release candidate. In both, I seem many instances of C00089 covale NAG D 2012 O4 NAG AM . O4 . BMA D 2013 C1 BMA AN . C1 . 'Custom glycosidic links need to be generated when the atom names of the carbohydrates don't conform to the standard.' for every glycan-glycan bond, but 'Taken from Monomer Library or GeoStd' for ASN-NAG, which does not make sense. The log file says the ALPHA1-3, ALPHA1-6, BETA1-4 and NAG-ASN links were properly applied, but the cif only mentions NAG-ASN. The cif also includes a link definition only for NAG-ASN, but none of the other glycosidic bonds. The structures appear to have proper geometry for glycosidic bonds, so this is probably just a cif-only issue. Also, is there a way to output the cif where every glycan residue does not get a new chain (this one goes up to chain AV=48 chains)? I found at least one phenix-refined case in the PDB where one glycan chain gets a single chain ID. Admittedly, that might have been fixed post phenix.refine. Thanks, Engin -- Engin Özkan, Ph.D. Associate Professor Dept of Biochemistry and Molecular Biology University of Chicago

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Two postdoc positions in Ubiquitin Signalling, WEHI, Melbourne, Australia
by Bernhard Lechtenberg 13 Jun '23

13 Jun '23

Dear colleagues, The Ubiquitin Signalling Division at The Walter and Eliza Hall Institute (WEHI) is looking to recruit two Research Officers (Postdocs) to join our teams in the Lechtenberg and Komander labs. WEHI in Melbourne is Australia’s pre-eminent medical research institute. The Ubiquitin Signalling Division at WEHI was established in 2018, and offers a vibrant, multi-disciplinary and highly collaborative environment at the forefront of ubiquitin research with access to state-of-the art facilities in proteomics, structural biology (Titan Krios G4, Australian Synchrotron), biophysics (SEC-MALS, ITC, SPR, mass photometry, MST), cell manipulation (CRISPR) and imaging facilities, and drug discovery through the National Drug Discovery Centre (NDDC). The division features a continuous stream of excellent publications, exciting preliminary data, and opportunities to establish research ideas in a multidisciplinary environment. The Lechtenberg lab seeks to recruit a postdoc with structural biology (crystallography or cryo-EM) and biochemistry expertise to study large RBR E3 ligase complexes. Preliminary data include an established mammalian expression system. Details and applications: https://wehi.wd3.myworkdayjobs.com/en-US/WEHI/job/Research-Officer---Struct… Contact: Dr. Bernhard Lechtenberg, lechtenberg.b(a)wehi.edu.au<mailto:[email protected]> The Komander lab seeks to recruit a postdoc with structural biology and protein biochemistry background to embark on an early-stage drug discovery project in the area of mitophagy and Parkinson’s disease, with excellent academic and translational / entrepreneurial outputs expected. Details and applications: https://wehi.wd3.myworkdayjobs.com/en-US/WEHI/job/Parkville-Victoria-Austra… Contact: Prof. David Komander, dk(a)wehi.edu.au<mailto:[email protected]> We offer three-year contracts with highly competitive salaries and benefits. Pre-application enquiries are encouraged via the contact details provided. Please share this information within your networks. Kind regards, Bernhard Bernhard C. Lechtenberg PhD NHMRC Emerging Leadership Fellow Laboratory Head Ubiquitin Signalling Division E lechtenberg.b(a)wehi.edu.au<mailto:[email protected]> T +61 3 9345 2217 [WEHI Logo] Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville Victoria 3052 Australia www.wehi.edu.au<https://wehi.edu.au> Twitter<https://twitter.com/WEHI_research> | Facebook<https://www.facebook.com/WEHIresearch/> | Instagram<https://www.instagram.com/wehi_research> | Youtube<https://www.youtube.com/user/WEHImovies> | LinkedIn<https://www.linkedin.com/company/wehi_research> WEHI acknowledges the Wurundjeri people of the Kulin Nation as the traditional owners of the land where our campuses are located and the continuing connection to country and community. Private and confidential The content of this e-mail and any attachments may be private and confidential, intended only for use of the individual or entity named. If you are not the intended recipient of this message you must not read, forward, print, copy, disclose, use or store in any way the information this e-mail or any attachment contains. If you are not the intended recipient, please notify the sender immediately and delete or destroy all copies of this e-mail and any attachment.

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Issue with running phenix.segment_and_split_map command
by Das, Abhinaba 11 Jun '23

11 Jun '23

Good afternoon all, I’ve been running Phenix using the GUI however I want to segment a map using phenix.segment_and_split_map which turns out to be a command line program. I’m trying to run it using the following command: abhinabadas@AbhinabasM1Mac ~ % phenix.segment_and_split_map \ /Users/abhinabadas/Downloads/Chimera/postProcessMaskedsharpened_map.ccp4 \ /Users/abhinabadas/Desktop/Test_map_2/rcsb_pdb_3J9G.fasta auto_sharpen = False \ box_in_auto_sharpen = False However, it ends every time giving the error: Read sequence from /Users/abhinabadas/Desktop/VipA-B/rcsb_pdb_3J9G.fasta Sorry: Need resolution for segment_and_split_map with sharpening Initially, I used the same command without using auto_sharpen = False box_in_auto_sharpen = False, as the map was already auto sharpened in Phenix. It gave me the same error regardless. Apologies for this possibly inane question; there might be a very easy fix to it but I can’t seem to figure it out. I would greatly appreciate any insights or suggestions to resolve this issue. Please let me know if you need any further information. Thank you for your attention and assistance. Thanks, abhi

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model symmetrisation
by Dmitry A. Semchonok 08 Jun '23

08 Jun '23

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2023 Cold Spring Harbor Macromolecular Crystallography Course
by Paul Adams 05 Jun '23

05 Jun '23

Dear Colleagues, The July 15th deadline for applications to the CSHL Macromolecular Crystallography Course to be held later this year, October 15th through October 31st 2023, is rapidly approaching. This is a unique opportunity to become expert in the use of crystallography to solve challenging macromolecular structures. The official course announcement can be found here: https://meetings.cshl.edu/courses.aspx?course=C-CRYS&year=23 please pass this on to anyone who you think might be interested and would benefit, especially students and postdocs. This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography, and consists of extensive lectures and practical sessions from experts in the field. The instructor team is: Janet Newman, Tom Peat, Jim Pflugrath, Dorothee Liebschner, and myself. We are assisted by world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation (see the course link above for more details). 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. We expect participants to crystallize one or more proteins and determine their structures in a two week period. Students may also work on their own projects, but not exclusively. They will become very well-versed in the theory of diffraction and crystal structure determination, while also having lots of fun. Both synchrotron data collection and in-house diffraction data collection will be used to solve structures. The course will also include the use of computationally predicted structures to aid in solving the crystallographic phase problem. The course is limited to 16 participants due to the very hands-on nature of the experiments and the intimate seminar and laboratory settings. Please check the above web link for more details. In particular, please note the information about the various fellowships, scholarships, and stipends that are available. The course is supported with funds provided by the National Institute of General Medical Sciences, for which we are extremely grateful. Also there are stipends available from the Leona M. and Harry B. Helmsley Charitable Trust and the Howard Hughes Medical Institute to help offset the cost of tuition. Scholarship support is also provided by Regeneron Pharmaceuticals. If anyone has any questions, please send me an e-mail, we will be happy to answer all queries. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov/leadership/) Principal Investigator, Computational Crystallography Initiative, LBL (https://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (https://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 33, Room 250 Building 978, Room 4126 Building 977, Room 268 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 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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AlphaFold button
by James Holton 30 May '23

30 May '23

Maybe I'm doing it wrong, but I was trying to show a class last week how to use the AlphaFold features of phenix, only to find that the Colab seems to no longer exist? I know the dedicated server is up now, but the current stable release does not have that feature in the GUI. Will a new stable release be released soon? Just asking, -James

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NCS operators
by Dmitry A. Semchonok 23 May '23

23 May '23

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real space R value calculation
by heinea＠mailer.uni-marburg.de 22 May '23

22 May '23

Dear mailing list, how can I calculate real space R-values fur individual residues or regions in a protein using Phenix? Any advice would be greatly appreciated. Thank you very much in advance, Andreas

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NCS operators
by Dmitry A. Semchonok 19 May '23

19 May '23

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