- phenixbb - phenix-online.org

Multiple conformations
by Alejandro Virrueta 25 Feb '16

25 Feb '16

This is not exactly phenix specific, but I was wondering what are some commonly used methods to determine and validate the presence/occurrence of multiple conformations for a given amino acid? I am currently refining (for 5 cycles) a pdb with the occupancy of atoms of a specific residue set to 0, and then looking at the difference density map contoured to 3 sigma for extra density. Is this somewhat correct? What else could/should I do? Would using OMIT maps help? (What are OMIT maps, and how do I generate them?) Thanks, Alex (not a crystallographer)

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How to include restrains to DNA as A-DNA or B-DNA
by Zhe Li 23 Feb '16

23 Feb '16

I am refining a protein-dsDNA complex structures at 2.4-3 A. Based on the phosphate distance, I can predict if particular nucleotide is A DNA (C3’-endo) or B DNA (C2’-endo). I want to add restrain to to the specific nucleotides as A or B DNA. But secondary_structure_restraints for nucleic acid does not seem to have options for this. Any suggestions? Thanks

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Course on “Integrating X-ray crystallography and scattering with electron microscopy” - Oeiras (Portugal)
by Jose Artur Brito 23 Feb '16

23 Feb '16

Dear Colleagues, we hereby announce a 4-day course on “Integrating X-ray crystallography and scattering with electron microscopy”. The course is funded by i-NEXT and will be held at NOVA ITQB, Oeiras (nearby Lisbon), Portugal, May 2 to 5, 2016. The course covers a multidisciplinary approach to study the structure of challenging proteins, focusing on membrane proteins and large complexes. The basic principles will be provided for each addressed technique (Macromolecular Crystallography, Mass Spectrometry and Electron Microscopy); their applications in biological systems, major benefits and limitations will also be discussed. The Workshop is organized with lectures in the mornings followed by hands-on training. The course is aimed primarily at PhD students and young Post-Doctoral researchers interested in Structural Biology. Confirmed speakers are Jose Maria Carazo, Dmitri Svergun and Isabel de Moraes. Participants will be limited to 20. Candidate selection will be based on a short CV, a motivation letter from the applicant, and a recommendation letter from the supervisor. Registration deadline is February 23. Please send your application to combstruct2016(a)itqb.unl.pt. Registration fee is 180Eur including accommodation. More information can be found at http://www.itqb.unl.pt/combstruct2016 The Organizers, Margarida Archer, José A. Brito (ITQB-UNL) and Jose Maria Carazo (CNB-CSIC) -- ************************************************** * Jose Artur Brito, PhD * * Post-Doctoral Fellow * * Membrane Protein Crystallography Laboratory * * Instituto de Tecnologia Quimica Biologica * * Avenida da Republica, EAN * * 2780-157 Oeiras * * PORTUGAL * * * * Telephone - +351 214 469 761 * * Mobile - +351 962 452 179 * * Fax - +351 214 433 644 * * * * E-mail - jbrito(a)itqb.unl.pt * * Website - http://mx.itqb.unl.pt/ * **************************************************

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CCP4 crystallographic summer school at the APS, June 21 - 29, 2016
by Sanishvili, Ruslan 23 Feb '16

23 Feb '16

Dear Colleagues, We are pleased to announce the 9th annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Title: CCP4 crystallographic school: From data collection to structure refinement and beyond Dates: June 21 through 29, 2016 Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises Data collection workshop the first three days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Crystallographic computation workshop: The rest of the time after data collection 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. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, 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 21. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Registration fees: The registration fee for the selected participants is $400 for the academic 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 reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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Rebuild fails in Rosetta-MR
by Rhys Grinter 22 Feb '16

22 Feb '16

Dear all, I'm currently trying to improve an model for a difficult MR problem using Rosetta-MR, When the program gets to the Rebuild stage it fails with the following message: *Error message:* child process stderr output: command: 'sh .../MR_ROSETTA_17/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/run_rebuild.sh"' .../MR_ROSETTA_17/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/run_rebuild.sh: line 5: 8996 Trace/BPT trap: 5 "/Applications/Rosetta/main/source/bin/mr_protocols.macosclangrelease" @"rebuild.flags" > "rebuild.log" 2>&1 Failed to run REBUILD Sorry: Failed to run REBUILD...see log file in .../MR_ROSETTA_17/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/rebuild.log Sorry: mr_rosetta failed... Sorry routine failed Please see log file for full error message *In the rebuild logfile:* dyld: lazy symbol binding failed: Symbol not found: ___sincos_stret Referenced from: /Applications/Rosetta/main/source/bin/mr_protocols.macosclangrelease Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___sincos_stret Referenced from: /Applications/Rosetta/main/source/bin/mr_protocols.macosclangrelease Expected in: /usr/lib/libSystem.B.dylib Has anyones experienced this error? Cheers, Rhys -- Dr Rhys Grinter Sir Henry Wellcome Fellow Monash University +61 (0)3 9902 9213 +61 (0)403 896 767

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Problem refining structure, error message
by Natalia Ketaren 22 Feb '16

22 Feb '16

Hello, I’m building a structure at the moment, and I have since removed lithium ions from structure. However, when I go to refine using phenix, I get the error message: “No atom selected: name LI and Chain F and rename LI resseq 8” I’ve tried using earlier files, prior to my addition of lithium ions and I still get the same error message. I’m using Phenix version 1.10.1-2155-000 Could anyone help me overcome this error message? Cheers, Nat _____________________________ Natalia E. Ketaren, PhD Research Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: (212) 327-8136 Fax: (212) 327-7193 Natalia.Ketaren(a)rockefeller.edu<mailto:[email protected]> website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/

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different occupancies for same molecule; optimize final model question
by Georg Mlynek 21 Feb '16

21 Feb '16

On 02/21/2016 11:33 PM, Georg Mlynek wrote: > Dear scientific community, > > 1. > > if I put in the gui under Modify selections for: Occupancies / simple > occupancy refinement > > resname SO4 > resname GOL > > > > phenix outputs different occupancies for each of the elements in the > molecule. > > > > Is the atom selection syntax wrong or is it a bug? (Ready set is also > not flagging or correcting this, would be nice is this can be implemented) > > 2. I used phenix optimize final model and I wonder why it refines K > anisotropic but not NA and CL. > (I would be very nice, if the program could summarize at the end which > settings and strategies were finally used, so this can be added to the > publication: I know it is under development) > > > adp { > individual { > isotropic = not (element K) > anisotropic = (element K) > } > > } > occupancies { > individual = resname NA or resname K or resname CL > remove_selection = None > constrained_group { > selection = None > } > > > I am using ubuntu 15.10 > > phenix version dev-2313-000 > > Many thanks in advance, best regards Georg.

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Fwd: Alternative method to Phenix_mr_rosetta
by Henry Fang 18 Feb '16

18 Feb '16

Hi All, Our group is working on an ab initial density modification method to solve the phase problem. Last year, I applied the methods to the cases with a initial template which has already been correctly placed in the unit cell. I tried several cases in the Terwilliger, T. C., et al. (2012). "phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta". Starting from the templates provided in the http://www.phenix-online.org/phenix_data/terwilliger/rosetta_2011/ I can get a initial density map, then apply our method to reduce the phase difference to around 50° in the highest experiment data resolution. Now, I might want to try more blind cases with our methods. If we can solve more structures, that would be more convincing. Do you have some suggestions? Where could I find some more unsolved structures? I might need structures with placed template and high solvent content (at least above 50%). Thanks, Henry

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Fwd: Generate difference electron density maps for residues with multiple conformations
by Alejandro Virrueta 18 Feb '16

18 Feb '16

Hello all, I am trying to get the difference electron density maps for residues with multiple conformations after I set the occupancy of their atoms to 0. My main goal is to visualize the green positive density peaks that should appear for the atoms whose occupancy I set to 0. However, when I run the phenix.refine command (doing all of this via cli, not gui), the output pdb file I will try to illustrate my process and problem with an example that works fine and one that doesn't, side by side, step by step. 1. I generate a pdb file that has a chosen residue set to occupancy 0. See 'pdb_1agy_res_SER_resID_120_del.pdb' and 'pdb_1agy_res_SER_resID_129_del.pdb'. As you can see, the former has SER 120 set to 0 occupancy and has one conformation, and the latter has SER 129 set to 0 occupancy for BOTH of its conformations. Both files are correct up to this point. 2. I then execute the following command: phenix.refine *pdb_del_file* *mtz_file* main.number_of_macro_cycles=5 output.write_eff_file=False output.write_geo_file=False output.write_def_file=False refinement.input.xray_data.r_free_flags.generate=True --overwrite - with *mtz_file *set to '1agy.mtz' (from the PDB) and *pdb_del_file* set to either 'pdb_1agy_res_SER_resID_120_del.pdb' and 'pdb_1agy_res_SER_resID_129_del.pdb'. - This results in 2 files pdb_1agy_res_SER_resID_XXX_del_refine_001.mtz and pdb_1agy_res_SER_resID_XXX_del_refine_001.pdb. Comparing these pdb files, you can see that the occupancy for SER 120 remains set to 0 (which is what I want), but the occupancies for the 2 conformers for SER 129 have been filled in by phenix (not what I want) somewhere during the refinement process. As a result, I get the desired difference peaks for SER 120, but not for SER 129 (which seems to be averaged out). Other than deleting the 2nd conformation for SER 129, is there a way to solve this problem, preferably via command line arguments/flags? Thanks, Alex

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correct space group for phenix.merging_statistics?
by Murpholino Peligro 18 Feb '16

18 Feb '16

Hi. Is it really important to have the correct space group in the mtz (or XDS_ASCII.HKL) file which will be the input for phenix.merging_statistics? I have space group= 89 And I know it is space group=96 Thanks

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