- phenixbb - phenix-online.org

naive question how to add GTP as a residue to a nucleic acid chain and refine!
by Almudena Ponce Salvatierra 13 Apr '19

13 Apr '19

Dear all, I would like to add a GTP residue to a nucleic acid chain. For so I followed the following steps in coot: add monomer from library, GTP, changed chain ID and residue number accordingly, and then Extensions --> Modelling --> link 2 atoms. I got a dashed line between the 3'O of the GTP and the phosphate of the neighboring nucleotide, and then I used the real space refine tool. Up to here, it all looked promising. In phenix refine I run elbow and readyset and provided cif files, but after phenix.refine I find out that the link between GTP and it's neighbor is gone. How to preserve the bond? Thank you very much in advance!! Best, Almudena

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12th CCP4/APS Crystallographic School in the US
by Xu, Qingping 12 Apr '19

12 Apr '19

Dear Colleagues, We are pleased to announce the 12th annual CCP4 crystallographic school “From data collection to structure refinement and beyond” will be held on June 17-24, 2019 at Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: http://www.ccp4.ac.uk/schools/APS-2019/index.php. Dates: June 17 through 24, 2019 Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises two parts: data collection workshop and crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, contact info and other details can be found at the School website. Applicants: Graduate students, postdoctoral researchers and early-career faculty, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 15th, 2019. To apply, visit https://www.ccp4.ac.uk/schools/APS-2019/application.php. Fees: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals). We hope to see you at the school. Charles, Garib and Qingping

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Re: [phenixbb] CryoFit run failure
by Kim, Doo Nam 12 Apr '19

12 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]>

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Faculty equivalent cryoEM position
by Hasan, Syed Saif 11 Apr '19

11 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

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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

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Clashscore and average B
by Sam Tang 09 Apr '19

09 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

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X-Ray Methods in Structural Biology @CSHL
by Paul Adams 06 Apr '19

06 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 ] --

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column labels for autobuild
by wtempel 05 Apr '19

05 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

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Re: [phenixbb] Phenix elbow taxol
by r.joosten＠nki.nl 05 Apr '19

05 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]>

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Tantalum cluster
by Alexandra Deaconescu 03 Apr '19

03 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

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