- phenixbb - phenix-online.org

Re: [phenixbb] CryoFit run failure
by Kim, Doo Nam 11 Apr '19

11 Apr '19

Hello Joseph, Sorry for late reply, your email was not in my inbox. I just changed my setting so that email to phenixbb(a)phenix-online.org will come to my inbox directly. Thank you for sharing your input file. I just ran your input pdb file, it appears that "SO4, "CD" are not in amber03 forcefield. I just added my comments like this Solution if these residue/atoms are important: Fix wrong names of atoms/residues. Running real_space_refine via phenix GUI will show which atoms need to be removed/fixed If gromacs amber03 force field doesn't have parameters for these residue/atoms, you may need to add parameters. It is rather a sad fact that most MD simulation force fields do not support all kinds of rare residue/atoms. cryo_fit2 is under development to address this issue using phenix.eLBOW Solution if these residue/atoms are not important: Remove these \"wrong\" atoms/residues from user's input pdb file. Run cryo_fit again Solution if your user's pdb file is big: Probably cryo_fit will change conformation just minimally, I would extract out these \"wrong\" atoms/residues from user's input pdb file, then add these extracted lines to cryo_fitted file If you do git pull at your <phenix>/modules/cryo_fit and run again, you will see results at least to the final stage (that I can't run because of lack of map). best regards, Doonam ________________________________ From: Finney, Joseph (NIH/NCI) [C] <joseph.finney(a)nih.gov> Sent: Monday, April 8, 2019 9:09:23 AM To: Kim, Doo Nam Cc: bugs-from-web(a)phenix-online.org; phenixbb(a)phenix-online.org; Esser, Lothar (NCI) Subject: CryoFit run failure Hey Doonam, As I said before I figured I would have some additional questions. The new version of phenix (1.15-3459-000) fixed my issues last week with the tutorial dataset. However, I am having trouble with our own testing dataset. As before we are testing in GUI version first. I am using the same run conditions for both the tutorial set and out testing set. I am attaching the log of the tutorial set as well as the log of our testing set and the test PDB. The density map is too large for email. The major error I see is “Step 1 didn't run successfully” from the ferrtest run. Looking at the tutorial PDB, it seems as though the header, the terminations, and the nonstandard atoms have been removed prior to use. I tried this and got a different error: “pdb file cleaning is not done, exit now” Do you have any recommendations on how to succeed? Thanks in advance! Joseph Finney [Contractor] Software Developer National Cryo-EM Facility Cancer Research Technology Program Frederick National Laboratory for Cancer Research Leidos Biomedical Research Inc. PO Box B Frederick, MD 21702 Tel: (301) 228-4313 Cell: (615) 512-2053 Joseph.finney(a)nih.gov<mailto:[email protected]>

1 0

Faculty equivalent cryoEM position
by Hasan, Syed Saif 10 Apr '19

10 Apr '19

************************************************************************************************** Faculty-Equivalent, Cryo-Electron Microscopy (Cryo-EM) Position Summary: As part of its program focused on advancing new measurement technologies and standards for biomolecular structure and function, the National Institute for Standards and Technology (NIST) Biomolecular Structure & Function Group seeks a ‘faculty-equivalent’ principle investigator to establish a research program focused on applications of cryo-electron microscopy (cryo-EM) in structural biology. We are particularly interested in candidates with a focus on developing cryo-EM experimental techniques and data analysis tools, and who would leverage other structure methods [e.g. nuclear magnetic resonance (NMR), macromolecular crystallography and/or small angle scattering], to advance the current state-of-the-art in structure-function analysis of biological systems of biopharmaceutical interest. The successful candidate should have a PhD or equivalent, a strong research portfolio and publication record that demonstrates evidence of cryo-EM expertise complementary to current group research strengths in NMR, crystallography and small angle scattering. He/she is expected to become a recognized leader in the field of cryo-EM and contribute to collaborative projects both within the group and with external partners. US Citizenship is required. The Biomolecular Structure & Function Group is located at the Institute for Bioscience and Biotechnology Research (IBBR<http://www.ibbr.umd.edu/>), a joint federal-state research partnership between NIST and the University of Maryland. IBBR operates state-of-the-art research facilities and is located in the heart of the biotechnology corridor in Rockville, Maryland. The Biomolecular Structure & Function Group is affiliated with the NIST Center for Neutron Research (NCNR<https://www.nist.gov/ncnr>) and the NIST Biomanufacturing<https://www.nist.gov/programs-projects/biomanufacturing-initiative> program. Our cryo-EM facility located at IBBR includes a newly installed 200 kV Talos-Arctica equipped with a Falcon III direct electron detector. A K3 direct electron detector and a Volta phase plate will be acquired soon in addition to a 200 kV Glacios microscope. State-of-the-art computational resources are available through the IBBR High Performance Computing Cluster. Salary: Commensurate with qualifications. Applications: Applicants should send cover letter, curriculum vitae, research statement, and contact information of three references to the attention of John P. Marino, Leader, Biomolecular Structure & Function Group: john.marino(a)nist.gov. ************************************************************************************************** S. Saif Hasan, PhD Assistant Professor Department of Biochemistry and Molecular Biology University of Maryland School of Medicine 108 N. Greene St., Baltimore, MD 21201 Group Leader Center for Biomolecular Therapeutics (CBT) Institute for Bioscience and Biotechnology Research (IBBR) 9600 Gudelsky Drive, Rockville, MD 20850 Phone: 240-314-6396 https://www.ibbr.umd.edu/profiles/s-saif-hasan

1 0

running phenix.validation from command line
by Roberto Marabini 09 Apr '19

09 Apr '19

Hi, I see that it is possible to execute phenix.validation from command line by typing: phenix.validation_cryoem <path to>/5ni1.cif <path to>/molprobity.mrc resolution=2.2 The program runs smoothly and prints on screen a few hundreds of lines. The more or less equivalent program in version 1.13 was phenix.molprobity, when executed with the option pickle=True, phenix.molprobity saved to the hard-disk a pkl file containing all data. Is there an equivalent flag for phenix.validation_cryoem? where is the result of executing this shell being saved? thanks Roberto

3 5

Clashscore and average B
by Sam Tang 08 Apr '19

08 Apr '19

Hello. I am refining a structure with Phenix.refine and encounter an issue which I appreciate your comments. The structure is in P1 and refined to 36A-3A. Rw/Rf = 23.9%/29.1%, RMS bonds 0.002, RMS angles 0.544, Ramachandran favoured 97.5%. The statistics is acceptable to me but two numbers raised my concern. First is the clashscore of 7.7, which is below minimum of other structures shown by Polygon. Second is an average B of 37, with a minimum of 9.2. When I checked again in Coot (Average Temp fact. analysis), none of the residues or water look abnormal. I refined both individual and group B-factors and applied 'Optimize X-ray/adp weight'. So my questions are: (1) if a clashscore too high means a lot of bad contacts, how do you comprehend a clashscore too low? How can I modify my strategy to get around? (2) is there an acceptable low value of B? (I sort of went through a similar thread in phenixbb appeared 9 years ago but seems the discussion did not come to a conclusion). Any advice I should reliax or tighten the adp restraints? PS - it may be worth mentioning the structure contains a OMU nucleotide. The .cif file I used was generated by elbow. The nucleotide looks normal in coot w.r.t. contact or B-value. Thanks a lot! Sam

2 2

X-Ray Methods in Structural Biology @CSHL
by Paul Adams 05 Apr '19

05 Apr '19

Dear All, The June 15th deadline for applications to the CSHL X-ray Methods in Structural Biology Course to be held later this year, October 15 through October 30, 2019 is rapidly approaching. The official course announcement is here: https://meetings.cshl.edu/courses.aspx?course=C-CRYS&year=19 so please pass this on to folks who might be interested and who would benefit. The course is designed for researchers who are either new to, or who wish to increase their in-depth knowledge of, macromolecular crystallography. This immersive course is an outstanding place to learn both the theoretical and practical aspects of Macromolecular Crystallography because of the extensive lectures from world-renowned teachers, which are combined with hands-on experiments. This 2019 course will be lead by Jim Pflugrath (Rigaku, ret.), Tassos Perrakis (NKI), Paul Adams (LBL), Janet Newman (CSIRO) and an All-Star cast of lecturers. Attendees can expect to participate in a course that is unparalleled in the world, with experts each devoting several days to teaching the fundamentals, theory and practical considerations of crystallographic structure solution. We expect to have the participants crystallize several proteins and determine their structures all in about two weeks.Students may also work on their own projects, but not exclusively. They will also become well-versed in the theory of X-diffraction and crystal structure determination while having lots of fun, but not much sleep. There will be a trip to the state-of-the-art beamlines at NSLS-II to collect data. The course is limited to 16 participants due to the very hands-on nature of the experiments and the intimate seminar room and laboratory settings. Please check the above web link for more details. In particular, please note the information about fellowships, scholarships, and stipends that are available. It is often possible for applicants to receive some level of support to help offset the course fee. This 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. If anyone has any questions, please send me e-mail, I will be happy to answer any queries. Thanks for spreading the word, Janet, Tassos, Paul, and Jim -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

1 0

column labels for autobuild
by wtempel 04 Apr '19

04 Apr '19

Hi all,how does one specify column labels in a definition file for phenix.autobuild? input_files { map_file_is_density_modified = True input_map_labels = “F PHIDM FOMDM” input_refinement_labels = “F SIGF FreeR_flag” } gives this error: Sorry: Sorry, the label 'F SIGF FreeR_flag' does not exist (or all data is zero) … ...available labels are: ['FreeR_flag', 'F', 'SIGF', 'FC', 'PHIC', 'FC_ALL', 'PHIC_ALL', 'FWT', 'PHWT', 'DELFWT', 'PHDELWT', 'FOM', 'FC_ALL_LS', 'PHIC_ALL_LS', 'PHIDM', 'FOMDM', 'FDM', 'None'] Many thanks in advance. Wolfram Tempel

2 1

Re: [phenixbb] Phenix elbow taxol
by r.joosten＠nki.nl 04 Apr '19

04 Apr '19

Before you make restraints yourself, check whether it is already in the dictionary. The name should be TA1 (http://ligand-expo.rcsb.org/reports/T/TA1/index.html). Cheers, Robbie On 31 Mar 2019 10:45, Georg Mlynek <georg.mlynek(a)univie.ac.at> wrote: Dear Ahmad, one way is to use the smiles string. If taxol if also named Paclitaxel then here it is: https://pubchem.ncbi.nlm.nih.gov/compound/paclitaxel#section=Canonical-SMIL… Then just watch this video on phenix.elbow https://www.youtube.com/watch?v=8qVYTUVKlbQ Br, Georg. On 31.03.19 08:08, Ahmad Khalifa wrote: How can I generate restraint files for taxol? I attached my taxol.pdb for reference. Thanks. _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]>

3 4

Tantalum cluster
by Alexandra Deaconescu 02 Apr '19

02 Apr '19

Hello, I am trying to phase off Tantalum clusters. According to the Phenix documentation online, one should use TX as a scatter in Hyss. However, this does not work and Phenix complains about "unknown scatter type." Any ideas how to solve this? Thank you, Alexandra -- Alexandra Deaconescu, B.E., Ph.D. Assistant Professor Brown University Office: (401) 863-3215 Wet Lab: (401) 863-6729 Computational Lab: (401) 863-7031

2 1

validation_cryoem
by Daniel Larsson 01 Apr '19

01 Apr '19

Hi, When I use the phenix.validation_cryoem command line tool, I get very little data compared to when I run the Cryo-EM validation from the GUI. Which options should I enable to get things like detailed clash annoation, CaBLAM analysis etc? Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

2 1

Phenix elbow taxol
by Ahmad Khalifa 31 Mar '19

31 Mar '19

How can I generate restraint files for taxol? I attached my taxol.pdb for reference. Thanks.

2 1

Call reminder: XChem fragment screening, NEXT WEDNESDAY
by Frank von Delft 29 Mar '19

29 Mar '19

Dear aspiring drug discoverers A reminder that the deadline for the next round of proposals for XChem fragment screening is *next Wednesday 5pm*, as part of Diamond's general Call for Proposals. Full details <https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening/Applying-for-XC…> are on the XChem webpage <https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening.html>. *Reminder: *we are now inviting a broader set of projects: * Two-tiered access: if you have an exciting system but don't yet know how to progress it, you can ask for exploratory access ("Tier 1") * BAG access: several labs and collaborations have requested increased flexibility, and several have been assigned Block Allocation Groups. If you wish to submit this route, I suggest you also email me directly. Happy screening! 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)

1 0

scattering_table in phenix.real_space_refine
by Keitaro Yamashita 25 Mar '19

25 Mar '19

Dear PHENIX developers, For the refinement of CryoEM structure, I changed scattering_table to electron from default (n_gaussian in phenix-1.13), but the resultant coordinates and ADPs were exactly same while map-model CCs were improved. Looking into the code, I noticed scattering_table is not passed to the ADP refinement code (mmtbx.refinement.real_space.adp.real_space_group_adp_refinery_via_reciprocal_space) and xray_structure is newly constructed from a pdb_hierarchy object; therefore a default table in scattering_type_registry() (which is n_gaussian) is always used. Is this an intended behavior? I modified the code to use the scattering table of electron in ADP refinement, and CCs were improved (CC_mask 0.7566 to 0.7813; both evaluated with scattering_table=electron). Best regards, Keitaro

2 1

Refinement
by StrBio 23 Mar '19

23 Mar '19

ALL. I have data at 2.4 A in P21 sp gr, helical protein. Refined to Rwork 29 Rfree 34 with nice density map and all nice statistics oither Rfactor (by Phenix). Refmac quit same. Should I deposit it or look better data? Any suggestion?

1 0

Phenix Rosetta hybrid refinement PHENIX_ROSETTA_PATH error
by Ahmad Khalifa 23 Mar '19

23 Mar '19

But I have the path set! (base) [labusr@luxor ~]$ echo $PHENIX_ROSETTA_PATH /home/labusr/rosetta:/home/labusr/rosetta/main I attached the log. Please advise.

2 1

Distance constraint to atom in symmetry copy in phenix.refine
by Julian Esselborn 22 Mar '19

22 Mar '19

Dear community, we have a somewhat complicated problem to which I don't seem to find a solution. We have a structure, which has a number of 3-fold and 2-fold symmetry axes in the final assembly structure. The 3-fold axes are hold together by metal atoms on the axis. However, we have three cases of these axes: 1. Symmetry axis falls onto the crystallographic symmetry axis. We can deal with this; setting metal to 0.33 occupancy and setting metal-protein distance constraints. This is a proper symmetry axis. 2. Symmetry axis doesn't fall onto a crystallographic symmetry axis, but all three monomers coming together are within the same symmetry copy of the ASU. Even easier, metal stays at occ=1 and we just set constraints to chain A, chain B, chain C. 3. The really challenging case, where the axis doesn't fall onto the symmetry axis, but the three monomers coming together are in different symmetry copies of the ASU. Cases (2) and (3) are pseudo-symmetric in the crystallographic sense. Usually a bit of intelligent moving around of the monomers to their crystallographic symmetry positions should push all monomers of case (3) into neighboring positions within the same ASU ending up as case (2); problem solved. BUT: In our structure we have too many 3fold axes, such that there will always be one of them ending up as case (3). E.g. the three monomers are chains A, B, C, but they do not end up neighboring in the ASU. Rather the axis is formed by A, B' and C'' (with ' denoting different symmetry copies of the ASU). We could assign the metal to chain A with occ=1 and no metal in B and C. However, we would need to set a distance constraint from the metal to it's ligands in protein monomer B and protein monomer C. But it is only the ligand in B' and C'', which are actually close to the metal in A. The ligands in B and C are at the other end of the ASU. Is there a way to set a distance constraint such that it measures the distance to a crystallographic symmetry copy? A different idea was to just assign an alternative position alt A, alt B and alt C to the metal, with A being close to the ligand in monomer A, B close to monomer B and C close to monomer C. That way we could make constraints. But we would need to cross fingers that the three metal atoms actually end up in the same spot once applying the crystallographic symmetry (and remember, that 3-fold axis is not constructed by applying a 3fold rotational symmetry around that axis; rather an actual crystallographic symmetry somwhere else brings them together; means the ligands with their metal atoms can actually move independently). I'm a bit at a loss how to deal with this and would appreciate input. Thanks a lot in advance! all the best Julian ---- Julian Esselborn Postdoctoral Researcher Tezcan group University of California, San Diego

3 6

Map Segmantation
by Yangqi Gu 21 Mar '19

21 Mar '19

Hi Everyone, I have a naive question about segmentation. I have a low resolution map of a filament (~20 A) and I know the helical symmetry. I have monomer sequence but no structure. I am wondering if I could segment the filament and obtain the monomer density? Does segment_and_split_map work on the low resolution case? Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

2 1

How to get command line of operation run through gui?
by Ahmad Khalifa 20 Mar '19

20 Mar '19

I'm trying to box out a cryo-em map and used the option "padding=" as per the documentation, but received error interpreting command line argument. is the documentation outdated? Regards.

1 0

mmCIF for deposition
by Patrick Loll 19 Mar '19

19 Mar '19

Hi all, Following the instructions given here: https://www.phenix-online.org/documentation/overviews/xray-structure-deposi… I’m attempting to use mmtbx.prepare_pdb_deposition to insert sequence information into the mmCIF that contains the model coordinates. Unfortunately, the program fails with an error (shown below). The sequence file is FASTA format, and contains an entry for each of the (4) chains in the AU, i.e. >A MSEQNCE… >B MSEQNCE… etc. Any bright ideas? ============this is what happens (vide infra)==================================== [PJL-iMac:blahblah/PJL_final] loll% mmtbx.prepare_pdb_deposition filename.cif seq_name.fasta Starting mmtbx.prepare_pdb_deposition on Mon Oct 1 11:16:23 2018 by loll =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, filename.cif Found sequence, seq_name.fasta Processing PHIL parameters: ------------------------------------------------------------------------------- No PHIL parameters found Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = “filename.cif" } default_model = “filename.cif" sequence_files = "seq_name.fasta" default_sequence = "seq_name.fasta" } Starting job =============================================================================== Validating inputs Using model: filename.cif Using sequence: seq_name.fasta Creating mmCIF block for sequence Traceback (most recent call last): File "/Applications/phenix-1.14-3260/build/../modules/cctbx_project/mmtbx/command_line/prepare_pdb_deposition.py", line 9, in <module> run_program(program_class=prepare_pdb_deposition.Program) File "/Applications/phenix-1.14-3260/modules/cctbx_project/iotbx/cli_parser.py", line 71, in run_program task.run() File "/Applications/phenix-1.14-3260/modules/cctbx_project/mmtbx/programs/prepare_pdb_deposition.py", line 98, in run alignment_params=self.params.mmtbx.validation.sequence.sequence_alignment) File "/Applications/phenix-1.14-3260/modules/cctbx_project/iotbx/pdb/hierarchy.py", line 1190, in as_cif_block_with_sequence assert len(chain.residue_groups) + chain.n_missing_start + chain.n_missing_end == len(sequence) AssertionError (gouts of smoke, terrified squealing) The ‘No PHIL parameters found’ message is concerning, but the program clearly seems to be finding the input file names. Suggestions welcome. Thanks, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pjloll(a)gmail.com pjl28(a)drexel.edu

3 4

FEM by using FoFc map
by Danilo Belviso 18 Mar '19

18 Mar '19

Dear all, I am interested in fitting a ligand in the case of a structure where water molecules have been already placed. I know that this is not the standard procedure, but these water molecules are quite sure. To do this, I used ligand fit procedure with command "lig_map_type = *fo-fc_difference_map fobs_map pre_calculated_map_coeffs" command. At the end, the procedure provides ligands with low CC (0.4-0.55). So, I would try ligand fitting by using FEM of Fo-Fc. The rationale is that FEM of Fo-Fc could help (likely) ligand fitting, by consider the presence of water molecules at the same time (Fo-Fc should be 0 where water molecules are placed). Maybe nothing will change, but I would try. I calculated FEM by using phenix.fem start_FEM.pdb start_FEM.mtz input.xray_data.label='FOFCWT' and also by using phenix.fem start_FEM.pdb start_FEM.mtz maps.map_coefficients_label='FOFCWT PHFOFCWT' file_name_prefix='FEM_map' where start_FEM.pdb and start_FEM.mtz are the pdb and mtz resulting from the refinement with water. However, by checking the the fem maps by coot, I notice that fem is completely different from Fo-Fc and it is not the expected feature-enanched Fo-Fc. Is the procedure and keywords correct to perform FEM calculation of Fo-Fc? Do you have any suggestions? Thanks Danilo -- Dr. Belviso Benny Danilo, PhD Istituto di Cristallografia (IC) Consiglio Nazionale delle Ricerche (CNR) via Amendola 122/o, 70126 Bari - Italy Tel ++39 080 5929273 Fax ++39 080 5929170 mail: danilo.belviso(a)ic.cnr.it web: users.ba.cnr.it/ic/crisdb00

2 1

UK Open Research Data Task Force weblink to Report, Case studies and Minister’s response
by John R Helliwell 18 Mar '19

18 Mar '19

Dear Colleagues, Thankyou for asking about the weblink to the case studies. The UK Open Research Data Task Force weblink to Report, Case studies and Minister’s response is here:- https://www.gov.uk/government/publications/open-research-data-task-force-fi… Best wishes, John

1 0

UK Open Research Data Task Force Final Report
by Jrh Gmail 17 Mar '19

17 Mar '19

Dear Colleagues, The UK Open Research Data Task Force Final Report is here:- https://assets.publishing.service.gov.uk/government/uploads/system/uploads/… This will be of general interest. As well as contributing to the general report I wrote the crystallography case study. Best wishes, John Emeritus Professor of Chemistry John R Helliwell DSc_Physics Chairman of IUCr Committee on Data

1 0

completeness issue
by yong zhou 17 Mar '19

17 Mar '19

Dear Pavel, Thanks for your reply. The output file is attached. Please check. Look forward to the reply. Best regards Yong Zhou ________________________________ From: Pavel Afonine <pafonine(a)lbl.gov> Sent: Tuesday, March 12, 2019 6:47 PM To: yong zhou; phenixbb(a)phenix-online.org Subject: Re: [phenixbb] completeness issue Can you send the file to me off-list? I'll have a closer look once I have the file. Pavel On 3/11/19 16:10, yong zhou wrote: Hi, Recently I deposited a structure to PDB. However, I was told there is a large difference between reported (77.89%) and calculated (88.36%) values for data completeness. In order to confirm the information, I used the command phenix.reflection_statistics and the result is as following. Resolution range: 31.6787 1.91132 Completeness in resolution range: 0.783333 Completeness with d_max=infinity: 0.783193 Anomalous completeness in resolution range: 0.599544 Bijvoet pairs: 15786 Lone Bijvoet mates: 9291 Mean anomalous difference: 0.0671 Space group of the intensities: P 2 2 2 Space group of the metric: P m m m Tolerance used in the determination of the lattice symmetry: 3 degrees Possible twin laws: None Completeness of 4-8-(GlcNAc)5/output4-8.sca:I(+),SIGI(+),I(-),SIGI(-): unused: - 31.6830 [ 0/9 ] 0.000 bin 1: 31.6830 - 1.9113 [28083/29673] 0.946 unused: 1.9113 - [ 0/0 ] There are two completeness values 0.783 and 0.946. So which is the correct one? Look forward to the reply. Yong Zhou _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]>

1 0

error in Phaser
by Alexandra Deaconescu 14 Mar '19

14 Mar '19

Hello, I have been trying to run Phaser using a map ensemble when I encountered the error listed below, which caused Phaser to fail. I have also attached the log file. Any help would be much appreciated. Thank you, Alexandra UNHANDLED ERROR: Program internal error in source file TraceMol.cc (line 229) *** Consistency check (wang_mask.size()) failed. ***

2 1

completeness issue
by yong zhou 12 Mar '19

12 Mar '19

Hi, Recently I deposited a structure to PDB. However, I was told there is a large difference between reported (77.89%) and calculated (88.36%) values for data completeness. In order to confirm the information, I used the command phenix.reflection_statistics and the result is as following. Resolution range: 31.6787 1.91132 Completeness in resolution range: 0.783333 Completeness with d_max=infinity: 0.783193 Anomalous completeness in resolution range: 0.599544 Bijvoet pairs: 15786 Lone Bijvoet mates: 9291 Mean anomalous difference: 0.0671 Space group of the intensities: P 2 2 2 Space group of the metric: P m m m Tolerance used in the determination of the lattice symmetry: 3 degrees Possible twin laws: None Completeness of 4-8-(GlcNAc)5/output4-8.sca:I(+),SIGI(+),I(-),SIGI(-): unused: - 31.6830 [ 0/9 ] 0.000 bin 1: 31.6830 - 1.9113 [28083/29673] 0.946 unused: 1.9113 - [ 0/0 ] There are two completeness values 0.783 and 0.946. So which is the correct one? Look forward to the reply. Yong Zhou

2 1

Re: [phenixbb] Fo-Fo difference map for non-isomorphous datasets
by Jordan Luke Pederick 11 Mar '19

11 Mar '19

Also, I am interested if anyone knows of any publications that have included a real-space difference map? Cheers, Jordan ________________________________ From: Jordan Luke Pederick Sent: Monday, 11 March 2019 1:25:57 PM To: Eric Montemayor; Pavel Afonine; Philip Kiser; Tim Gruene; phenixbb(a)phenix-online.org Subject: Re: [phenixbb] Fo-Fo difference map for non-isomorphous datasets Thank you all for the prompt responses and suggestions. My metal ion of interest is Cesium in this case, so I guess I am more interested in using this approach for visualization rather than peak identification - the strong density of Cs is fairly obvious I have attached a few images of the superimposed (Fo, Phi) maps and resulting difference map using either Superpose maps in phenix or transform_map in coot following Tim's suggestions. I also tried using maprot (CCP4) to apply the rotation/translation operator from the LSQ superpose but the resulting map was not superposed correctly (not sure why). Both results seem kind of reasonable - I have shown one of the difference peaks for what is likely to be a bound Cs. For both approaches the peak was very obvious at a 3 sigma level, and could still be observed to around 10 sigma in both cases. I am still unsure about differences in scaling, so although strong positive peaks can be identified, I wouldn't be confident using the map to interpret smaller differences. In response to Eric - I checked the anomalous signal, which was fairly weak. The resulting anomalous difference map did show positive peaks up to a level of ~10 sigma that matched those observed in the above real-space difference maps, with a 3 sigma level corresponding to 0.0137 e/A^3. The CCanom was also low (1-5% between shells), so I was thinking that another approach might be more suitable for this data? Cheers, Jordan ________________________________ From: Eric Montemayor <montemayor.eric(a)gmail.com> Sent: Sunday, 10 March 2019 4:50:21 AM To: Jordan Luke Pederick Subject: Re: [phenixbb] Fo-Fo difference map for non-isomorphous datasets Why not just look for peaks in the anomalous difference Fourier for just the derivative dataset? If there’s even a weak anomalous signal, you won’t need to mess with non-isomorphism between multiple datasets.... the information you need is already contained alone in the derivative dataset. What is the metal? The above approach won’t work for something like magnesium, but should work for almost any transition metal. Eric On Sat, Mar 9, 2019 at 3:23 AM Jordan Luke Pederick <jordan.pederick(a)adelaide.edu.au<mailto:[email protected]>> wrote: Hi, I am trying to generate a Fo-Fo difference map for two data sets of the same protein at ~2.3 angstrom resolution. One dataset is native and the other was soaked with a metal ion, so the purpose of the map is for identifying and visualizing peaks that may correspond to a bound metal ion. These datasets differ by 6 angstroms (~10%) along the A edge - an isomorphous difference map generated in Phenix GUI wasn't useful As an alternative I was planning to make a real-space Fo-Fo difference map making use of Superpose Maps in Phenix Gui as follows: Superpose maps would be used to superimpose (Fobs.metal, PHI.metal) and (Fobs.native, PHI.native) The superimposed maps will be opened in Coot and a difference map generated using "Extensions -> Maps -> Make a difference map" There were two things I was unsure about: Does this seem like a reasonable alternative? Is scaling of the two datasets required before generating the difference map? Cheers, Jordan _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]>

1 0

phenix.elbow error
by Eugene Osipov 10 Mar '19

10 Mar '19

Dear phenix developers, I have found that QM calculations in phenix.elbow fail due to an error: *bad fp number.* I've found the source of the error in phenix-1.14-3260/modules/elbow/elbow/quantum/run_utils.py at line 11: easy_run.call('./%s.csh >& /dev/null' % project) should be : easy_run.call('./%s.csh 2>&1 /dev/null' % project) Also jaguar template (phenix-1.14-3260/modules/elbow/Jaguar.csh) is a bit outdated. For $SCHRODINGER/jaguar paramether -PROC was replaced by -PARALLEL also, it seems that programs seeks for wrong input file. So I suggest that: $SCHRODINGER/jaguar run -PROCS %d -WAIT $PROJECT should look like: $SCHRODINGER/jaguar run -PARALLEL %d -WAIT $PROJECT.in Can you please fix this issues in next releases? -- Evgenii Osipov Laboratory for Biocrystallography, Department of Pharmaceutical Sciences, KU Leuven O&N2

2 1

Fo-Fo difference map for non-isomorphous datasets
by Jordan Luke Pederick 09 Mar '19

09 Mar '19

Hi, I am trying to generate a Fo-Fo difference map for two data sets of the same protein at ~2.3 angstrom resolution. One dataset is native and the other was soaked with a metal ion, so the purpose of the map is for identifying and visualizing peaks that may correspond to a bound metal ion. These datasets differ by 6 angstroms (~10%) along the A edge - an isomorphous difference map generated in Phenix GUI wasn't useful As an alternative I was planning to make a real-space Fo-Fo difference map making use of Superpose Maps in Phenix Gui as follows: Superpose maps would be used to superimpose (Fobs.metal, PHI.metal) and (Fobs.native, PHI.native) The superimposed maps will be opened in Coot and a difference map generated using "Extensions -> Maps -> Make a difference map" There were two things I was unsure about: Does this seem like a reasonable alternative? Is scaling of the two datasets required before generating the difference map? Cheers, Jordan

3 2

Units in intensity?
by Murpholino Peligro 09 Mar '19

09 Mar '19

If I do `phenix.xtriage XDS_ASCII.HKL` I get a log file. In the "Statistics for data merging" of this log file I have: Resolution: 26.02 - 1.40 Observations: 44675 Unique reflections: 16306 Redundancy: 2.7 Completeness: 70.37% Mean intensity: 1656.8 Mean I/sigma(I): 19.8 SigI < 0 (rejected): 644 observations R-merge: 0.027 R-meas: 0.032 R-pim: 0.017 My question is... what units does Mean intensity has? Thanks Ps I am not sure if this has to do with the detector used which was a CCD (type) ADSC QUANTUM 210 (model).

3 5

difference in Wilson B calculated in Xtriange or Polygon
by Eze Chivi 08 Mar '19

08 Mar '19

Hi, The value of Wilson B calculated in Phenix differs for the same data when I use Polygon or Xtriange, why? In Xtriange-->Absolute scale and Wilson analysis: ML estimate of overall B value: 48.88 A**2 In Polygon: 52.05 Thank you Ezequiel

1 0

contour values for Polder and FEM
by V F 07 Mar '19

07 Mar '19

Hi all, What is the recommended values for contouring for Polder and FEM? In pymol, I have a isomesh polder_COA_mesh, polder_207_1, 3, select_COA, carve=2 isomesh FEM_COA, fem_coa_190, 1, select_COA, carve=2 Are these sensible values? Many thanks, Vero PS: Both identify ligand very well!

2 1

AUC2019 – registrations are open.
by Renwick Dobson 06 Mar '19

06 Mar '19

Dear Structural Biology community, AUC2019<https://auc2019.uleth.ca/>, the 24th AUC Workshop and Symposium, will be held at the University of Canterbury, Christchurch (New Zealand) from 24-29 August 2019. The format of the event is a 2-3 day workshop<https://auc2019.uleth.ca/workshops.php> offering parallel, hands-on training in experimental design and the latest AUC data analysis software from the world experts in this area followed by a 2 day research symposium on AUC and complementary approaches: methodological development, combination with orthogonal techniques (SAXS, SANS, SPR, MST, SEC-MALLS etc), application in biosciences and material sciences. Registrations are now open and details can be found at this website: https://auc2019.uleth.ca/ As the scientific program<https://auc2019.uleth.ca/symposium.php> for AUC2019 emerges, events will be uploaded to the website. We strongly encourage you to submit abstracts for talks and posters<https://auc2019.uleth.ca/abstracts.php>. The meeting is also timed such that delegates can also attend the Queenstown Molecular Biology Conference<https://www.queenstownresearchweek.org/> (which is in Queenstown), although note that this is a separate conference. Lastly, The European Biophysics Journal has kindly agreed to run a special issue to celebrate the research presented at AUC2019. Therefore, we invite those who wish to extend their talks to a journal publication to consider contributing original research articles to this issue. Please indicate your interest for inclusion in this volume below. Deadline for registration of a contribution is August 30 2019. We look forward to welcoming you to Christchurch, New Zealand next Spring(-ish)! Ren Dobson, Chair AUC2019 On behalf of the AUC2019 Scientific Organising Committee ---- Prof. Ren Dobson Co-Director, Biomolecular Interaction Centre (BIC) http://www.bic.canterbury.ac.nz/ School of Biological Sciences | Te Kura Pūtaiao Koiora University of Canterbury | Te Whare Wānanga o Waitaha Private Bag 4800 Christchurch | Ōtautahi New Zealand | Aotearoa E: renwick.dobson(a)canterbury.ac.nz<mailto:[email protected]> T: ++64 (03) 369-5145 x 95145 F: ++64 (03) 364-2590 W: http://dobsonlab.org/

1 0

Postdoctoral position in structural biology of influenza virus transcription Cusack group, EMBL Grenoble
by Stephen Cusack 05 Mar '19

05 Mar '19

Postdoctoral position in structural biology of influenza virus transcription Cusack group, EMBL Grenoble We are looking for a highly motivated and ambitious individual to progress our understanding of the mechanism of transcription by influenza virus RNA-dependent RNA polymerase. The work is in the frame of the ANR-funded FluTranscript project that brings together the complementary expertise of the groups of Stephen Cusack (EMBL Grenoble, project coordinator) and Nadia Naffakh (Institut Pasteur) in structural biology and molecular virology, respectively. The project follows on from a recent joint publication (Structural basis of an essential interaction between influenza polymerase and Pol II CTD. Lukarska et al, Nature 2017) and aims to reconstitute and determine the structure of functional transcription complexes. A secondary goal is to use the acquired structural information to develop new approaches to anti-influenza drug development. The Cusack group uses X-ray crystallography and cryo electron-microscopy to study the structural biology of protein-RNA complexes involved in RNA virus replication, innate immunity and cellular RNA metabolism. Group website: https://www.embl.fr/research/unit/cusack/index.html The successful candidate should have a PhD in Molecular Biology or related field and a strong background and interest in biochemistry and structural biology. We are looking for a creative and ambitious person with good communication skills and keen to work on a challenging project. Experience in insect cell expression systems, reconstitution of protein-RNA complexes, X-ray crystallography or cryo-electron microscopy would be particularly beneficial. EMBL is one of the world’s leading research organizations in the life sciences. The Headquarters Laboratory is located in Heidelberg, with additional sites in Barcelona, Grenoble, Hamburg, Hinxton, and Rome. EMBL Grenoble has excellent access to state-of-the-art structural biology technologies with the in house EM facility being equipped with a T12 microscope and 200kV Glacios/Falcon III . Additionally, we have access to the Titan Krios at the adjacent ESRF as well as those in EMBL Heidelberg. Other facilities on the Grenoble Campus include the ESRF synchrotron X-ray beamlines, neutron scattering at the ILL, high-field NMR at the IBS as well as high-throughput crystallization platform, mammalian and insect cell facilities, biophysical platform and confocal microscopy. You can find out more about this vacancy at: https://www.embl.fr/jobs/searchjobs/index.php?ref=GR00133 or by contacting Stephen Cusack: cusack(a)embl.fr Please apply online through www.embl.org/ Stephen Cusack -- ********************************************************************** Dr. Stephen Cusack, FRS Head of Grenoble Outstation of the European Molecular Biology Laboratory (EMBL) Group leader in structural biology of protein-RNA complexes and viral proteins ********************************************************************** Email: cusack(a)embl.fr Website: http://www.embl.fr Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7123 Fax: (33) 4 76 20 7199 Postal address: EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue des Martyrs, 38000 Grenoble, France **********************************************************************

1 0

Are TLS parameters applied when TLS refinement is OFF?
by Mark Saper 04 Mar '19

04 Mar '19

I have a structure where at one stage TLS parameters were determined and then refined. It caused the R-free to increase so I stopped refining the TLS parameters. Are the TLS parameters still applied to the structure on subsequent refinement runs even when the TLS refinement is off? Is it appropriate to refine anisotropic B’s for a high resolution (1.35 Å) structure AND apply TLS parameters? Thanks, Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III saper(a)umich.edu +1 (734) 764-3353 mobile: (734) 276-6505

2 3

MAD merged dataset deposition
by Eugene Osipov 03 Mar '19

03 Mar '19

Hello, everyone, I have solved the structure of heme containing protein using anomalous signal from Fe atom (~1.739 anstroms) and further refined it using native dataset (0.9 angstroms). Structure was solved in AutoSol. The question is "What is the best way to deposit mtz with both datasets?" Should I merge and scale them simultaneously or can I deposit output file from AutoSol overall_best_refine_data.mtz, which contains F,FP, Rfree and HL coefficients? P.S.: please, respond in PM, I have only digest subscription on phenixBB. Thank you in advance! -- Evgenii Osipov Laboratory for Biocrystallography, Department of Pharmaceutical Sciences, KU Leuven O&N2

2 1

Rotamer restraints in phenix.real_space_refine
by Ashley Pike 28 Feb '19

28 Feb '19

Hi - Am I right in thinking that rotamer restraints behaves differently in latest official release (1.14-3260) compared to last but one official release (1.13-2998)? Issuing rotamer_restraints=True from command line or GUI used to give 0% rotamer outliers in the molprobity analysis at end of log in 1.13-2998 but now in 1.14 gives non-zero for same input model. It is as if they are not being applied. In the old log file it used to clearly print - **Update rotamer restraints*** after every macrocycle, in the 1.14 logs this is omitted. Many thanks, Ashley

3 4

molprobity in phenix 1.14
by Roberto Marabini 25 Feb '19

25 Feb '19

Hi, In the past (phenix 1.13) I have been able to execute molprobity with the command line: ============== phenix.python /usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py /home/roberto/sda/ScipionUserData/projects/TestMolprobityValidation2/Runs/000170_PhenixProtRunMolprobity/extra/5ni1.cif map_file_name=/home/roberto/sda/ScipionUserData/projects/TestMolprobityValidation2/Runs/000170_PhenixProtRunMolprobity/extra/molprobity.mrc d_min=2.200000 pickle=True pdb_interpretation.clash_guard.nonbonded_distance_threshold=None nproc=4 pdb_interpretation.clash_guard.nonbonded_distance_threshold=None ================== Unfortunately, for version 1.14 I get the error: ========================== Traceback (most recent call last): File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py", line 310, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py", line 193, in run map_params=params) File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/validation/molprobity/__init__.py", line 216, in __init__ molprobity_map_params=map_params.input.maps) File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/validation/experimental.py", line 198, in __init__ from mmtbx.command_line.map_model_cc import get_fsc ImportError: No module named map_model_cc ============== That is, there is an error in the line "from mmtbx.command_line.map_model_cc import get_fsc" By the way, if I just run the command: ============== phenix.python /usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py /home/roberto/sda/ScipionUserData/projects/TestMolprobityValidation2/Runs/000170_PhenixProtRunMolprobity/extra/5ni1.cif ================== the program is executed without any problem. What should I do in order to execute molprobity.py with the option map_file_name. best wishes Roberto

2 1

real space refine generates non-compliant PDB files
by Edwin Pozharski 22 Feb '19

22 Feb '19

Not sure whether anyone would care now that we got our marching orders to abandon PDB format and move to mmCIF, but the output of phenix.real_space_refine includes a number of lines that are not legit PDB records, i.e. this section ... REMARK 3 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.004 0.049 74053 ANGLE : 0.747 12.299 100513 CHIRALITY : 0.052 0.232 11312 PLANARITY : 0.006 0.069 13125 DIHEDRAL : 11.589 179.958 44947 MIN NONBONDED DISTANCE : 2.276 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 5.04 RAMACHANDRAN PLOT: OUTLIERS : 0.30 % ALLOWED : 8.63 % FAVORED : 91.06 % ROTAMER OUTLIERS : 8.76 % CBETA DEVIATIONS : 0 PEPTIDE PLANE: CIS-PROLINE : 3.7037037037 CIS-GENERAL : 0.0 TWISTED PROLINE : 1.85185185185 TWISTED GENERAL : 0.316455696203 REMARK 3 ... This does result in errors when this output PDB file is used as input to other software that is more stringent with format compliance. Cheers, Ed.

2 1

Junior group leader opportunity in infection research (Braunschweig, Germany)
by Blankenfeldt, Wulf 22 Feb '19

22 Feb '19

Dear colleagues, I'd like to bring your attention to a job opening for a junior research group leader at the Helmholtz Centre for Infection Research in Braunschweig, Germany. The opening is broadly for infection research, and structural biologists should also feel encouraged to apply. The HZI has state-of-the-art facilities for x-ray crystallography and, through our participation in the CSSB on the DESY campus in Hamburg, to cryo-EM. We also have a protein sample production facility and equipment for biochemical/biophysical characterization. More details about the position and application requirements (deadline Feb. 28th!) can be found here: https://www.nature.com/naturecareers/job?id=672825 Best regards, Wulf ________________________________ Helmholtz-Zentrum f?r Infektionsforschung GmbH | Inhoffenstra?e 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling Stellvertreter: MinDirig R?diger Eichel, Nieders?chsisches Ministerium f?r Wissenschaft und Kultur Gesch?ftsf?hrung: Prof. Dr. Dirk Heinz; Silke Tannapfel Gesellschaft mit beschr?nkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

1 0

run phenix.refine in command line error
by 张士军 18 Feb '19

18 Feb '19

Dear I cannot run the *.params file when I use command line to run phenix.refine. Does have any default *.params file format, which I can edit it according to my case? Can you sent me one if does exist? Thanks . Best regards Shijun

1 0

error installation dev-1.14.3405 - 1.14.3409
by Guenter Fritz 13 Feb '19

13 Feb '19

Dear phenix developers, I get errors trying to install latest builds from 1.14.3405, 3406, 3409 64bit centos6 on Scientific Linux machines still running 6.6 (kernel 2.6.32). 1.14.3395 installed without any problem. The downloaded file is OK. 1.14.3409 64bit centos6 installed on Ubuntu 18.04 without any problem. I also tried to install from source but got the same error output (see below). I googeled some error outputs - looks like some python error. Do I have to update finally? Best regards, Guenter Output trying to install from source: [guenter@msm68 phenix-installer-dev-3409-source]$ ./install --prefix=/home/software/PHENIX/1.14.3409/ --nproc=10 Traceback (most recent call last): File "./bin/install.py", line 20, in <module> from libtbx.auto_build import install_distribution File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/install_distribution.py", line 75, in <module> from libtbx.auto_build import install_base_packages File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/install_base_packages.py", line 28, in <module> from .package_defs import * File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/package_defs.py", line 18, in <module> from .bootstrap import Toolbox File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/bootstrap.py", line 14, in <module> import argparse ImportError: No module named argparse Similar from an installer: [guenter@msm68 phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6]$ ./install --prefix=/home/software/PHENIX/1.14.3405/ Traceback (most recent call last): File "./bin/install.py", line 20, in <module> from libtbx.auto_build import install_distribution File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 75, in <module> from libtbx.auto_build import install_base_packages File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_base_packages.py", line 28, in <module> from .package_defs import * File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/package_defs.py", line 18, in <module> from .bootstrap import Toolbox File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/bootstrap.py", line 14, in <module> import argparse ImportError: No module named argparse

2 4

CryoEM post-doctoral position
by Hasan, Syed Saif 07 Feb '19

07 Feb '19

A post-doctoral research position is high-resolution single particle cryoEM is available immediately in my laboratory at the Institute for Bioscience and Biotechnology Research (IBBR; https://www.ibbr.umd.edu/profiles/s-saif-hasan) in Rockville MD. The post-doctoral researcher will have a choice of multiple projects in structural biology of membrane protein complexes involved in cancer and viral pathogenesis. The researcher will have independence to guide the direction of their research and to pursue novel ideas should they find an interesting scientific question related to the general focus of my laboratory. IBBR is home to a large community of structural biologists. Our new cryoEM facility houses a 200 keV Thermo Fisher Talos Arctica microscope equipped with a Gatan K3 direct electron detector. A 200keV Thermo Fisher Glacios microscope equipped with a Falcon III direct electron detector will be acquired soon. A 120 keV FEI Tecnai T12 TEM equipped with a CCD camera is available for negative stain imaging. In addition to the latest cryoEM facilities, IBBR offers access to tools in X-ray crystallography, NMR, small angle X-ray scattering, mass-spectrometry and computational biology, and provides opportunities to work closely in collaboration with scientists in industry and in national labs located nearby (i.e., NIH, NIST). Applicants should have experience in sample preparation, data collection and data processing for single particle cryoEM. Applicants who have received their PhD or MD/PhD degree should email me (sshasan(a)som.umaryland.edu) a single PDF file containing a short cover letter (no more than one page), a detailed curriculum vitae, contact information for three references, and up to 3 reprints of representative first authorship publication(s). The University of Maryland, Baltimore is an Equal Opportunity, Affirmative Action employer. Minorities, women, individuals with disabilities and protected veterans are encouraged to apply. S. Saif Hasan, PhD Assistant Professor Department of Biochemistry and Molecular Biology University of Maryland School of Medicine 108 N. Greene St., Baltimore, MD 21201 Institute for Bioscience and BiotechnologyResearch (IBBR) 9600 Gudelsky Drive, Rockville, MD 20850 https://www.ibbr.umd.edu/profiles/s-saif-hasan

2 1

Real space vs reciprocal refinement
by Maheshwaran.V 03 Feb '19

03 Feb '19

Dear phenixbb! In the current version of phenix.refine contains the separate option for refinement: xyz (reciprocal space) and xyz (real space ). What does it mean and how it differs from the previous versions which had xyz and real space instead. So I just wanted to know what does it actually do? Can we run both of them simultaneously? Is it advisable to do both refinement for DNA ? - Mahesh India.

1 0

Re: [phenixbb] Occupancy larger than 1
by Schnicker, Nicholas J 31 Jan '19

31 Jan '19

Hi Andrew, You should use group constrained refinement to link the occupancies of each isomer. You can see the documentation for how to implement it. https://www.phenix-online.org/documentation/reference/refinement.html#occup… Cheers, Nick From: <phenixbb-bounces(a)phenix-online.org> on behalf of Andrew Philip Thompson <andrew.thompson(a)adelaide.edu.au> Date: Wednesday, January 30, 2019 at 10:18 PM To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: [phenixbb] Occupancy larger than 1 Hi Phenix BB, We discovered that a fragment had degraded in our crystallography condition and the product was observed bound in the resulting crystal structure. Unfortunately we have been unable to separate certain stereoisomers of this compound or its analogues, and so are looking to simultaneously model two of the isomers into the crystal structure. I have made a .cif file corresponding to each isomer and modelled them into my crystal structures with altloc tags A & B, however after refinement, the occupancy of the two adds up to more than 1 in some instances (ie. 0.51 and 0.53). I’ve never had this before when trying to model dual conformations of the stereoisomers. I tried to make the ligands the same residue number as discussed in a previous thread (http://www.phenix-online.org/pipermail/phenixbb/2011-March/016859.html), however neither coot or pymol will open the pdb file after refinement if I do this. Unfortunately I am unable to share the pdb file as we do not want to disclose the compound structure. Does anyone have any suggestions as to how to proceed? Thanks in advance, Andrew Andrew Thompson PhD Candidate Molecular and Cellular Biology School of Biological Sciences The University of Adelaide, Australia

3 2

Occupancy larger than 1
by Andrew Philip Thompson 30 Jan '19

30 Jan '19

Hi Phenix BB, We discovered that a fragment had degraded in our crystallography condition and the product was observed bound in the resulting crystal structure. Unfortunately we have been unable to separate certain stereoisomers of this compound or its analogues, and so are looking to simultaneously model two of the isomers into the crystal structure. I have made a .cif file corresponding to each isomer and modelled them into my crystal structures with altloc tags A & B, however after refinement, the occupancy of the two adds up to more than 1 in some instances (ie. 0.51 and 0.53). I’ve never had this before when trying to model dual conformations of the stereoisomers. I tried to make the ligands the same residue number as discussed in a previous thread (http://www.phenix-online.org/pipermail/phenixbb/2011-March/016859.html), however neither coot or pymol will open the pdb file after refinement if I do this. Unfortunately I am unable to share the pdb file as we do not want to disclose the compound structure. Does anyone have any suggestions as to how to proceed? Thanks in advance, Andrew Andrew Thompson PhD Candidate Molecular and Cellular Biology School of Biological Sciences The University of Adelaide, Australia

1 0

using phenix.refine results in coot on another computer
by Christian Biertuempfel 30 Jan '19

30 Jan '19

Dear all, I often run phenix.refine on a server but I would like to use the results on my laptop for further manual building. Is it possible to somehow export the todo lists (outliers/problems) identified in phenix.refine/molprobity as a script in order to use them in coot on another computer? Alternatively, is it possible to open the results from phenix.refine in a gui with coot integration on another computer (without access to the original data partition)? Cheers, christian ____________________________________________________________________ Dr. Christian Biertümpfel Max Planck Institute of Biochemistry Molecular Mechanisms of DNA Repair Am Klopferspitz 18 phone: +49 89 8578 3641 82152 Martinsried fax: +49 89 8578 3605 Germany ____________________________________________________________________

2 1

IUCr Congress 2020 in Prague programme planning; data aspects
by John R Helliwell 29 Jan '19

29 Jan '19

Dear Colleagues, I draw your attention to the planning of IUCr Congress 2020 in Prague for which I am assisting with the programme planning on the data aspects:- http://forums.iucr.org/viewtopic.php?f=39&t=41 The Programme Committee is listed here:- http://www.iucr25.org/ipc/list.htm All best wishes, John Emeritus Professor John R Helliwell DSc Chairman of the IUCr Committee on Data

3 2

unrestrained refinement
by Kaiser, Jens T. 28 Jan '19

28 Jan '19

Hi! I'm trying to do unrestrained refinement of a small molecule in phenix. I have done this many years ago, but it seems whatever I try, phenix.refine now complains about missing nonbonded energy type for all atoms. The pdb file I supply has the following format (just one line) HETATM 33 C81 UNK 1 3.117 14.425 18.765 1.00 1.45 C I tried unchecking all references to geometry restraints in the GUI, setting wc and wu to 0 I also started from a default .eff file and set all references to restraints to either True of False (depending what they said). I also tried the line from the phenix.refine documentation: phenix.refine ../cif_in/mkt_a.ent ../data/181119/proc/137C3/XDS_17000.HKL strategy=individual_sites wc=0 refinement.input.symmetry_safety_check=warning refinement.input.xray_data.r_free_flags.generate=True I'm using phenix v 1.14-3260 from an sbgrid environment. Any pointers welcome. Cheers, Jens

3 4

Announcement: SpringerBriefs in Crystallography
by Dorothee Liebschner 28 Jan '19

28 Jan '19

Hi everyone, I would like to circulate the announcement of a new series of crystallography monographs entitled “SpringerBriefs in Crystallography” ( https://www.springer.com/series/16236). Areas of interest include structural biology. The announcement below is on behalf of the editor-in-chief, Prof. M. Nespolo. Best wishes, Dorothee Liebschner Series editor for biological crystallography, SpringerBriefs in Crystallography ========================================= Dear Colleagues, It is my pleasure to announce the launch of a new series of crystallography monographs under the title “SpringerBriefs in Crystallography”. They cover a new discipline within the “SpringerBriefs” collection, which publishes concise monographs with an intermediate scope ( https://www.springer.com/gp/authors-editors/book-authors-editors/springerbr… ). SpringerBriefs already covers 84 fields spanning a wide range from natural sciences to law, social sciences and more; crystallography is now the 85th field. The new series is published under the auspices of the International Union of Crystallography and all the manuscripts will be peer-reviewed by the series editors, as well as external reviewers when necessary. It takes an intermediate and so far uncovered place between articles published by the IUCr journals and full monographs. The IUCr publishes several types of articles in its journals (https://journals.iucr.org): • Research Papers, which are full-length manuscripts that normally do not exceed 15 journal pages (about 15 000 words); • Short Communications, for the presentation of topics of limited scope or for preliminary announcements of novel research findings; • Lead Articles, authoritative, comprehensive and forward-looking reviews of major areas of research interest (by invitation); • Feature Articles, focused surveys covering recent advances in an area of current research, which do not aim to be comprehensive, and are generally about ten journal pages (10 000 words); • Topical Reviews, which aim to capture the current trends of a field and are expected to be relatively short (about 6000 words and a maximum of 50 references, with half of those having been published in the last three years); • Letters to the Editor, which may deal with non-technical aspects of crystallography, its role, its propagation, the proper function of its Societies etc. • Scientific Commentaries, which discuss articles of particular importance for the readership of the journal. Full monographs spanning hundreds of pages are published in the IUCr/OUP monographs, and textbooks in the IUCr/OUP texts (https://www.iucr.org/publications/iucr-oup). SpringerBriefs in Crystallography aims at publishing shorter monographs, typically between 50 and 125 pages, where specific topics are dealt with more in detail with respect to what one could do in a Lead Article or Topical Review, in particular with a more pronounced accent on the background. Also, more space is given to some fundamentals which would not find place in a Lead Article or Topical Review, with the aim of providing the reader a more pedagogical introduction (whenever suitable) without the need to look for it in a separate text. Publications in this series help support the Outreach and Education Fund for the International Union of Crystallography (https://www.iucr.org/iucr/sponsorship/iucr-outreach-fund). The website of the new series is available at the address https://www.springer.com/series/16236, where you find more details as well as the responsible editor contact information, who upon request can provide you with a proposal form. On submission the responsible editor will then forward it to the series editors for discussion and approval. Please, feel free to forward this information to your colleagues who may be interested in publishing a monograph in this series. -- Project Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

1 0

This is a test
by Billy Poon 28 Jan '19

28 Jan '19

The Phenix website was down for a few hours, so this is a test to see if the bulletin board is working. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

1 0

Announcement: SpringerBriefs in Crystallography
by Dorothee Liebschner 28 Jan '19

28 Jan '19

Hi everyone, I would like to circulate the announcement of a new series of crystallography monographs entitled “SpringerBriefs in Crystallography” ( https://www.springer.com/series/16236). Areas of interest include structural biology. The announcement below is on behalf of the editor-in-chief, Prof. M. Nespolo. Best wishes, Dorothee Liebschner Series editor for biological crystallography, SpringerBriefs in Crystallography ========================================= Dear Colleagues, It is my pleasure to announce the launch of a new series of crystallography monographs under the title “SpringerBriefs in Crystallography”. They cover a new discipline within the “SpringerBriefs” collection, which publishes concise monographs with an intermediate scope ( https://www.springer.com/gp/authors-editors/book-authors-editors/springerbr… ). SpringerBriefs already covers 84 fields spanning a wide range from natural sciences to law, social sciences and more; crystallography is now the 85th field. The new series is published under the auspices of the International Union of Crystallography and all the manuscripts will be peer-reviewed by the series editors, as well as external reviewers when necessary. It takes an intermediate and so far uncovered place between articles published by the IUCr journals and full monographs. The IUCr publishes several types of articles in its journals (https://journals.iucr.org): • Research Papers, which are full-length manuscripts that normally do not exceed 15 journal pages (about 15 000 words); • Short Communications, for the presentation of topics of limited scope or for preliminary announcements of novel research findings; • Lead Articles, authoritative, comprehensive and forward-looking reviews of major areas of research interest (by invitation); • Feature Articles, focused surveys covering recent advances in an area of current research, which do not aim to be comprehensive, and are generally about ten journal pages (10 000 words); • Topical Reviews, which aim to capture the current trends of a field and are expected to be relatively short (about 6000 words and a maximum of 50 references, with half of those having been published in the last three years); • Letters to the Editor, which may deal with non-technical aspects of crystallography, its role, its propagation, the proper function of its Societies etc. • Scientific Commentaries, which discuss articles of particular importance for the readership of the journal. Full monographs spanning hundreds of pages are published in the IUCr/OUP monographs, and textbooks in the IUCr/OUP texts (https://www.iucr.org/publications/iucr-oup). SpringerBriefs in Crystallography aims at publishing shorter monographs, typically between 50 and 125 pages, where specific topics are dealt with more in detail with respect to what one could do in a Lead Article or Topical Review, in particular with a more pronounced accent on the background. Also, more space is given to some fundamentals which would not find place in a Lead Article or Topical Review, with the aim of providing the reader a more pedagogical introduction (whenever suitable) without the need to look for it in a separate text. Publications in this series help support the Outreach and Education Fund for the International Union of Crystallography (https://www.iucr.org/iucr/sponsorship/iucr-outreach-fund). The website of the new series is available at the address https://www.springer.com/series/16236, where you find more details as well as the responsible editor contact information, who upon request can provide you with a proposal form. On submission the responsible editor will then forward it to the series editors for discussion and approval. Please, feel free to forward this information to your colleagues who may be interested in publishing a monograph in this series. -- Project Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

1 0