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phenix-1.15.2-3472 crashes with multiple CIF's
by oleg＠quantumbioinc.com 03 May '19

03 May '19

phenix-1.15.2-3472 crashes at the very end of the refinement when multiple CIF's are given at the command line (see below). Please have a look. Thanks Oleg Borbulevych, Ph.D. Staff Scientist QuantumBio, Inc. 2790 W. College Ave. State College, PA 16801 E-mail: oborbulevych(a)yahoo.com, oleg(a)quantumbioinc.com Linkedin Professional Profile: https://www.linkedin.com/in/oleg-borbulevych-b8045422 ============================== Exporting results ============================== Writing refined structure to PDB file: /home/oleg/TEST2/astex/full_set/astex_oniom_qm5_5_01_19/1N2J/1N2J-H_refine_001.pdb n_use = 9639 n_use_u_iso = 9639 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 9639 Writing refined structure to CIF file: /home/oleg/TEST2/astex/full_set/astex_oniom_qm5_5_01_19/1N2J/1N2J-H_refine_001.cif Traceback (most recent call last): File "/home/oleg/phenix-1.15.2-3472/build/../modules/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/home/oleg/phenix-1.15.2-3472/modules/phenix/phenix/refinement/command_line.py", line 162, in run refine_object.write_model_cif_file(f_cif_model) File "/home/oleg/phenix-1.15.2-3472/modules/phenix/phenix/refinement/driver.py", line 984, in write_model_cif_file additional_blocks=[cif_block]) File "/home/oleg/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/model/model.py", line 964, in model_as_mmcif restraints = self.extract_restraints_as_cif_blocks() File "/home/oleg/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/model/model.py", line 862, in extract_restraints_as_cif_blocks if '_chem_comp_plane_atom.comp_id' in loop.keys(): AttributeError: 'NoneType' object has no attribute 'keys'

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 02 May '19

02 May '19

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission for the July 2019 issue is 20 May 2019. The previous issue is available http://phenix-online.org/newsletter/ and contains the following. January 2019 <http://phenix-online.org/newsletter/CCN_2019_01.pdf> Short Communications - MARCO: The Machine Recognition of Crystallization Outcomes <http://phenix-online.org/newsletter/CCN_2019_01.pdf#page=7> - Building a model the way you do: Map-to-model version 2 <http://phenix-online.org/newsletter/CCN_2019_01.pdf#page=9> Fitting tips #16 – Asn and Gln are remarkably different <http://phenix-online.org/newsletter/CCN_2019_01.pdf#page=1> FAQ - Are the defaults the best for refinements? <http://phenix-online.org/newsletter/CCN_2019_01.pdf#page=6> The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.phenix-2Donline.org…>. Cheers Nigel Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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geometry_restraints.edits.scale_restraints
by Wei Wang 02 May '19

02 May '19

Dear PHENIX developers, I would like to know if the refinement.geometry_restraints.edits.scale_restraints still a valid option for tightening local restraints. I didn’t see this option from the phenix —show-defaults=all. I saw this option on the FAQ webpage. thx Wei

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Phaser Small Molecule MR
by Whitley, Matthew J 02 May '19

02 May '19

Hello all, We have collected electron diffraction data to approximately 1.8 Å on a 'small molecule' of roughly 1660 Da. The space group (P 43 21 2) and unit cell parameters determined during data reduction match the known, published values, and our data are roughly 80% complete in all resolution shells from 17 - 1.8 Å. We would like to solve this structure by molecular replacement in Phaser, but are having a bit of difficulty doing so. Our problems all seem to be related to specifying the composition of the target molecule for Phaser. Via the phenix GUI, we can only specify the target composition as either protein or nucleic acid, when in fact the target is neither. The chemical composition of the target is C72 H85 N19 O18 S5. Is there a way to feed this chemical composition to Phaser and to get it to understand that the target is neither protein nor nucleic acid? Furthermore, according to our reading of the Phaser documentation, specifying "protein" leads to an assumed solvent content of 50%, which is likely to be a substantial overestimation for this small molecule crystal. We have also run into the problem of Phaser complaining that the target molecule will not fit into the given unit cell, which we think is due to the assumption of 50% solvent content. We would be thankful for whatever advice you may have on using Phaser with non-protein, non-nucleic acid molecules. Matthew --- Matthew J. Whitley, Ph.D. Research Instructor W. Furey Lab Department of Pharmacology & Chemical Biology University of Pittsburgh School of Medicine

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Phenix elbow unable to determine bonding
by Ahmad Khalifa 01 May '19

01 May '19

I'm not sure why I'm getting this error. I generated restraint files for GDP with no problems. I noticed that if I change the coordinates of my files, I have to regenerate a new restraint files to match the new coordinates. This time I'm getting this error that I couldn't troubleshoot: Please find attached my gdp.pdb. --------- ['/storage/IJ/.phenix/project_data/elbow_88.eff'] --------- <function run at 0x7fbd2b4bb938> Working parameter elbow { input { chemical_file_name = None chemical_file_name_type = *auto pickle chemical_string = None chemical_string_type = *smiles sequence geometry_file_name = /storage/00_Marina_Ahmad/Tubulin/real_space_refinement/GDP.pdb geometry_file_name_usage = *topology initial orientation final assist template_file_name = None chemical_components_code = None residue = None read_only = False do_all = False optimisation_choice = None *auto am1 mogul ampac gamess gaussian jaguar \ mopac nwchem orca qchem } defaults { id = """GDP""" name = None pH = low *neutral high random_seed = None add_hydrogens = None write_hydrogens = True write_redundant_dihedrals = False multiple_planes = False auto_bond_cutoff = 1.95 pdb_attributes { resseq = 1 icode = None chain_id = A } } optimisation { steps = None tolerence = loose *default tight memory = 1000Mb energy_validation = None third_party_apps { nprocs = 1 method = *uhf mp2 b3lyp basis = *am1 sto-3g 3-21g 6-31g 6-31g(d) 6-31g(d,p) aux_basis = None } } view { view_results = *None reel molden pymol } output { no_output = False output = None output_dir = /storage/00_Marina_Ahmad/Tubulin/real_space_refinement/ pass_through_input_restraints = None pass_through_library_restraints = None output_file_formats = *pdb *cif pdb_ligand tripos sdf data_sheet png xyz \ maestro data_header_file = "" job_title = """GDP""" overwrite = False console_output = *default quiet silent chiral = *retain both enumerate pucker = *random enumerate define pucker_definition = "" cis_trans = *retain enumerate png = False } special { regno = None secondary_smiles = None amgen_id = None } non_user_parameters { opt_type = simple input_type = pdb_rich use_template = False } } ------------------------------------------------------------------------------ electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.14-3260 None - Nigel W. Moriarty (NWMoriarty(a)LBL.Gov) ------------------------------------------------------------------------------ Option opt_type not available Option input_type not available Option job_title not available Option use_template not available Random number seed: 3628800 Initial processing time : 0.00 seconds 0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing P Input format is PDB MoleculeClass : C:10 N: 5 O:11 P: 2 (PDB format) 28 atoms 30 bonds 0 angles 0 dihedrals 0 rings 0 chirals Predicted memory usage by semi-empirical method : 45Mb Timing estimates Python portion / ATP : 86% c++ optimisation cycle / ATP : 76% 0:00 Bondise Bondise Bondise Bondise Bondise Bondise Bondise Bondise Bondise B Failed to determine the bonding of a fragment of the molecule. PDB file elbow.GDP.GDP_pdb.001.pdb written. Bonding file elbow.GDP.GDP_pdb.001.bonding.py written. Edit bonding file to reflect the desired bond. ALTERNATIVELY Re-run eLBOW with the --reel option and the molecule wil be loaded into REEL. Edit the bonds and save the results as "fixed.cif" to allow eLBOW to load the bonding. You can also use a pull-down menu to push to eLBOW.

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NIH/NSF-Funded Research Specialist Position in Structural Biology at the University of Illinois at Chicago
by Yury Polikanov 01 May '19

01 May '19

NIH/NSF-Funded Research Specialist Position in Structural Biology at the University of Illinois at Chicago The Polikanov Laboratory at the University of Illinois at Chicago (IL, USA) is looking for talented, skillful, and highly motivated researchers to fill the NIH/NSF-funded Visiting Research Specialist positions to study the structure and function of the bacterial ribosome. The research in the Polikanov Laboratory 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. More information about Dr. Polikanov research can be obtained from the most recent publications ( https://www.ncbi.nlm.nih.gov/sites/myncbi/yury.polikanov.1/bibliography/503…) or found on the laboratory web-page ( https://bios.uic.edu/bios/people/faculty/yury-polikanov). The successful candidate will be involved in determination of high-resolution structures of ribosome functional complexes with various protein translation factors, tRNAs, and antibiotics using macromolecular X-ray crystallography techniques. Basic qualifications: • BS degree in chemistry, biochemistry, biophysics, or a related field is required; • MS degree or higher is preferred;• Minimum of 3 years of laboratory research experience is required; • Strong background in biochemistry and molecular biology is required; • Practical skills with the most standard methods currently used in molecular biology, and biochemistry (such as protein expression, purification); • Experience in structural biology (cryo-EM or X-ray crystallography) is not required but is highly desirable; • Experience in RNA biology field is not required but is highly desirable; The successful candidate is also expected to: • Act independently in terms of planning and executing the experiments; • Compile, analyze, and prepare data for publications; • Assist with training of graduate and undergraduate students. Interested candidates should submit their CV, cover letter, and contact information for three references at https://jobs.uic.edu/job-board/job-details?jobID=113640&job=visiting-resear… by June 28, 2019. Cover letter should be describing how previous research accomplishments and scientific interests of a candidate fit with the scope of the research in the Polikanov Lab. The University of Illinois at Chicago is an Equal Opportunity, Affirmative Action employer. Minorities, women, veterans and individuals with disabilities are encouraged to apply. The University of Illinois may conduct background checks on all job candidates upon acceptance of a contingent offer. Background checks will be performed in compliance with the Fair Credit Reporting Act *Jacquelyn DeLaurentis* *Human Resource Associate* *Department of Biological Sciences* *The University of Illinois at Chicago* *845 W Taylor St. * *3238 SES, MC 066* *Chicago, IL 60607* *(312) 996-2213 * *jdelaur(a)uic.edu <jdelaur(a)uic.edu>* [image: UIC Logo]

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modelling into positive densities
by Sam Tang 30 Apr '19

30 Apr '19

Hello, I am refining a structure solved to 1.5A by MR. Rw/Rf were 0.17/0.22 which seem acceptable to me. At the very beginning part of the protein the electron density is a bit wobbly. I am able to build the residues into the positive densities. But after phenix.refine the chain always shifts away a bit and leaves the green blobs there. (Photo: https://drive.google.com/open?id=1UngAJuEUt1S0LwPybMJLw2E1xA4cNM3R) I am thinking if this can be solved by adjusting the target weights. Or can I apply certain restraints only to those few residues? I refined XYZ (reciprocal space), XYZ (real space), individual B-factors, TLS and occupancies. Thanks in advance. Regards Sam

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molprobity vs validation_cryoem
by Roberto Marabini 28 Apr '19

28 Apr '19

Hi guys, We are using phenix version 1.15.2-3472. We have executed molprobity using the command line: phenix.python_1.15.2-3472 /usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/command_line/molprobity.py "path_to_pdb"/refmac-refined.pdb pickle=True nproc=4 We have also executed validation_cryoem (here we have used both the GUI and the command line and both interfaces return the same result) phenix.python_1.15.2-3472 ./phenix/phenix/command_line/validation_cryoem.py "path_to_pdb"/refmac-refined.pdb "path_to_map"/molprobity.mrc resolution=3.2 pickle=True What we do not fully understand is why the two commands return different results for molprobity. Are the default parameters different? For example, validation_cryoem reports as number of outliers "34" in the molprobity tab (model.geometry.angle.outliers) while molprobity reports 21 The test files are available at: 3Dmap: https://drive.google.com/open?id=0B_i_LJfUN1z7amoyM1B2N1U0Y2VYODB6LWdLY1pwa… pdb file: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5093775/ Thanks for the help

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weak anomalous phasing (magic triangle I3C)
by ChenTiantian 25 Apr '19

25 Apr '19

Dear all, I'm working on a 18kD protein, the secondary structure prediction says most of the structure is beta sheets, trying to solve the structure with SAD. Heavy atom soaking gives several datasets with I, W, Au, range from 2.7~3.7A, however, the anomalous signal is pretty weak, I couldn't find a reasonable solution. We got a co-crystal dataset with the magic triangle I3C, extends to around 2.5A, this is the best data we got so far. shelxc gives me the following result: Resl. Inf. 12.59 7.75 5.84 4.77 4.08 3.59 3.22 2.94 2.70 2.51 2.35 N(data) 79 257 429 635 811 1010 1235 1384 1698 1555 1954 Chi-sq 0.69 0.63 0.60 0.67 0.61 0.88 1.05 1.02 0.80 0.55 0.42 <I/sig> 79.4 34.1 30.3 32.2 31.8 26.6 21.1 14.6 8.3 3.9 2.4 %Complete 94.0 98.1 97.5 99.5 99.4 99.0 99.7 100.0 99.9 85.4 96.1 Multipl. 4.0 4.5 3.9 4.5 4.7 4.2 4.4 4.8 5.0 4.3 4.4 R(pim)% 2.27 1.72 2.29 2.05 2.02 2.62 3.51 4.84 7.90 14.43 22.78 Ranom% 6.49 3.68 5.19 4.29 4.27 6.35 9.50 12.97 20.90 33.58 52.21 <d"/sig> 0.73 0.80 1.08 0.85 0.95 1.03 1.00 0.91 0.85 0.78 0.70 CC(1/2) 5.1 41.7 68.8 38.1 42.7 49.9 49.9 25.5 24.9 13.3 -4.7 then I tried shelxd with different heavy atom sites number and resolution cut, the best CC I got is CC/CCweak: 24.75/7.69, and I can identify a triangle, (length: 6.5/6.5/5.0A), however, both shelxe and autosol didn't end up with a promising result. [image: image.png] It would be great if anyone can give me some suggestions. Thank you in advance! -- Tiantian

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2 positions around XChem-related compound design
by Frank von Delft 24 Apr '19

24 Apr '19

Dear all, I have two open to work on fragment/XChem-related methodology for structure-based compound design. Team Leader (applications close next *Weds 1st May*): full ad here <https://www.thesgc.org/careers/oxford/sgc-oxford-team-leader-xchem>, summary: /We are recruiting an experienced computational chemist or scientific programmer, to head the Fragalysis project for automating fragment hit progression, part of the XChem collaboration between SGC and Diamond... The //Fragalysis <https://fragalysis.diamond.ac.uk/>//project leader will be tasked with converting the existing proof-of-concept tool into a production-level system that is routinely usable for analysing XChem results and designing and acquiring follow-up compounds. This will entail setting the scientific direction and priorities of the project through close and continuous interaction with expert and novice users; coordinating a growing team of scientific programmers and contractors; liaising with and expanding a wide and international set of collaborators and contributors; securing further funding for the project; helping supervise students; and developing specific methodologies of their own./ Postdoc (closing *Weds 15th May*): full advert here <https://www.thesgc.org/careers/oxford/sgc-oxford-postdoctoral-research-scie…>, this is a summary: /This role will be tasked with the design and acquisition of follow-up compounds based on fragment screening hits from the Target Enabling Package (//www.thesgc.org/tep <http://www.thesgc.org/tep>//) and Ultra-DD (//www.ultra-dd.org <http://www.ultra-dd.org>//) programs. The successful candidate will coordinate experimental validation of the newly designed compounds with collaborating scientists in order to progress them towards potent molecules. / Cheers Frank -- Prof Frank von Delft Associate Professor Principal Investigator: Protein Crystallography Structural Genomics Consortium Oxford University +44 1865 617583 (office: W,F) Principal Beamline Scientist: I04-1 Diamond Light Source +44 1235 778997 (office: M,T,T) +44 7471 026103 (mobile)

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