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Refining peptides with beta-amino acids
by Bram Mylemans 26 Jun '23

26 Jun '23

Dear experts, I’m trying to refine a crystal structure of a peptide that contains some beta-amino acids. I have tried generating restraints with elbow from a sdf file. I changed the naming of the atoms to conform with the protein naming and added the L-peptide linking tag. This seems to work for refining and also local refine in coot works. However, the peptide bond is not kept planar. Does anyone have an idea how to make sure the amide bond is correctly constrained? I have included the restrained file I made for L-beta-Leucine below for reference. Best wishes, ---------- Dr. Bram Mylemans Post-doctoral Research Associate Woolfson group School of Chemistry University of Bristol # electronic Ligand Builder and Optimisation Workbench (eLBOW) # - a module of PHENIX version 1.20.1-4487- # - file written: Sun May 14 14:31:25 2023 # # Inital geometry file: a 60 line input string # Ligand name: (3S)-3-amino-5-methylhexanoic acid # Quantum optimisation: True # Method: uhf # Random seed: 3628800 # SMILES string: CC(C)C[C@H](N)CC(O)=O # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level B3L B3L '(3S)-3-amino-5-methylhexanoic acid' L-peptide 24 10 . # data_comp_B3L # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.charge _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z B3L O O O 0 -0.621 -0.0468 -0.0672 0.0379 B3L C C C 0 0.403 1.2030 -0.0409 -0.0524 B3L CA C CH2 0 -0.215 2.0004 0.0099 1.2717 B3L CB C CH1 0 0.109 1.5936 -1.1463 2.1941 B3L N N NH2 0 -0.452 2.4198 -2.3233 1.9111 B3L CG C CH2 0 -0.173 1.7636 -0.6462 3.6485 B3L CD C CH1 0 -0.040 1.5804 -1.7407 4.6994 B3L CE2 C CH3 0 -0.160 1.9937 -1.1916 6.0651 B3L CE1 C CH3 0 -0.159 0.1402 -2.2497 4.7124 B3L HA H HCH2 0 0.055 3.0941 0.0115 1.0876 B3L HAA H HCH2 0 0.036 1.7870 0.9871 1.7352 B3L HB H HCH1 0 0.088 0.5145 -1.4120 2.0199 B3L HN H HNH2 0 0.153 1.9179 -3.1939 1.9355 B3L HG H HCH2 0 0.049 2.7650 -0.1815 3.7540 B3L HGA H HCH2 0 0.063 1.0542 0.1844 3.8432 B3L HD H HCH1 0 0.048 2.2575 -2.6020 4.4708 B3L H3E2 H HCH3 0 0.033 2.4606 -1.9617 6.6915 B3L H2E2 H HCH3 0 0.049 2.7302 -0.3796 5.9910 B3L H1E2 H HCH3 0 0.045 1.1543 -0.7788 6.6358 B3L H3E1 H HCH3 0 0.045 0.0304 -3.1957 4.1675 B3L H2E1 H HCH3 0 0.034 -0.2410 -2.4354 5.7240 B3L H1E1 H HCH3 0 0.068 -0.5687 -1.5528 4.2450 B3L OXT O OC -1 -0.606 1.8564 -0.0003 -1.1279 B3L HNA H HNH2 0 0.147 3.2587 -2.3840 2.4671 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd B3L C O single 1.253 0.015 B3L C OXT single 1.259 0.016 B3L CA C single 1.546 0.037 B3L CB CA single 1.534 0.036 B3L CB HB single 1.125 0.040 B3L N CB single 1.466 0.036 B3L N HNA single 1.008 0.037 B3L CG CB single 1.547 0.037 B3L CG HG single 1.109 0.039 B3L CD CG single 1.528 0.035 B3L CD CE1 single 1.528 0.035 B3L CE2 CD single 1.529 0.035 B3L CE2 H1E2 single 1.096 0.038 B3L CE1 H1E1 single 1.098 0.038 B3L CE1 H3E1 single 1.097 0.038 B3L HA CA single 1.109 0.037 B3L HAA CA single 1.102 0.040 B3L HN N single 1.005 0.037 B3L HGA CG single 1.110 0.039 B3L HD CD single 1.119 0.040 B3L H3E2 CE2 single 1.097 0.038 B3L H2E2 CE2 single 1.099 0.038 B3L H2E1 CE1 single 1.097 0.038 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd B3L OXT C CA 117.56 2.401 B3L CA C O 116.95 2.270 B3L OXT C O 125.42 1.837 B3L HAA CA HA 105.03 2.935 B3L HAA CA CB 111.34 2.722 B3L HA CA CB 111.25 2.583 B3L HAA CA C 106.82 2.670 B3L HA CA C 111.50 2.415 B3L CB CA C 110.69 2.417 B3L HB CB CG 109.11 2.657 B3L CG CB N 112.27 2.657 B3L HB CB N 108.74 2.657 B3L CG CB CA 107.01 2.247 B3L N CB CA 109.86 2.386 B3L HB CB CA 109.83 2.388 B3L HNA N HN 110.49 3.000 B3L HN N CB 114.17 2.677 B3L HNA N CB 114.27 2.682 B3L HGA CG HG 104.29 2.953 B3L HGA CG CD 109.80 2.649 B3L HG CG CD 110.06 1.813 B3L HGA CG CB 109.67 2.659 B3L CD CG CB 113.69 2.657 B3L HG CG CB 108.91 2.671 B3L HD CD CE1 108.40 2.672 B3L HD CD CE2 107.17 2.674 B3L CE1 CD CE2 111.53 2.389 B3L HD CD CG 109.76 2.723 B3L CE2 CD CG 108.95 2.259 B3L CE1 CD CG 110.95 2.656 B3L H1E2 CE2 H2E2 105.67 2.934 B3L H2E2 CE2 H3E2 105.78 2.934 B3L H1E2 CE2 H3E2 107.05 2.933 B3L H2E2 CE2 CD 112.73 2.662 B3L H3E2 CE2 CD 111.91 2.665 B3L H1E2 CE2 CD 113.17 2.686 B3L H1E1 CE1 H2E1 106.00 2.935 B3L H2E1 CE1 H3E1 106.10 2.936 B3L H1E1 CE1 H3E1 105.73 2.935 B3L H2E1 CE1 CD 113.07 2.437 B3L H3E1 CE1 CD 112.17 2.708 B3L H1E1 CE1 CD 113.17 2.649 # loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period B3L Var_01 CB CA C O 54.55 30.0 2 B3L Var_02 CE1 CD CG CB -66.07 30.0 1 B3L Var_03 H1E1 CE1 CD CG -19.34 30.0 3 B3L Var_04 H1E2 CE2 CD CG 93.46 30.0 3 # loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign B3L chir_01 CB CA N CG negativ # loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd B3L plan-1 O 0.020 B3L plan-1 C 0.020 B3L plan-1 CA 0.020 B3L plan-1 OXT 0.020

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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 10 Jun '23

10 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 07 Jun '23

07 Jun '23

2 1

2023 Cold Spring Harbor Macromolecular Crystallography Course
by Paul Adams 04 Jun '23

04 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

3 3

real space R value calculation
by heinea＠mailer.uni-marburg.de 21 May '23

21 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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