May 2017 - phenixbb - phenix-online.org

Questions on TLS output and more info on phenix.tls
by Michael Garavito 29 May '17

29 May '17

I am finishing the final stages of refinement with TLS at 1.7 Å and want to begin some B-factor analysis. Also, I am setting up for a series of ensemble refinements. However, I am second guessing myself and have been finding that several basic questions that are not explicitly answered by the Phenix documentation. (1) Just to be sure, I looked for the definition of what is written in the ATOM records of the output PDB file after refinement with TLS: residual B or total B (residual B + TLS contribution). I always thought the latter after refinement with TLS, but nothing was explicitly stated. (2) Also, I have looked for it extensively in the Phenix documentation, I have not found any information on phenix.tls, even though in several places (e.g., phenix.ensemble_refinement), there are explicit references to phenix.tls: “If TLS is used the TLS components must be present in the atom records (see phenix.tls)” The information from just doing % phenix.tls -h does not give enough insight into options and there use. Can someone point me to the right place to get these answers? Thanks, Michael **************************************************************** R. Michael Garavito, Ph.D. Professor of Biochemistry & Molecular Biology 513 Biochemistry Bldg. Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334 Email: garavito(a)msu.edu ****************************************************************

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Linking C-Type Heme
by Julian Esselborn 23 May '17

23 May '17

Hi list, that might sound like a stupid question, but we are having some trouble getting phenix.refine acknowledging a c-type linkage of a heme. That is a covalent Cys SG bond to C18 or C25 in the heme. The pdb file does contain a LINK record for this, but Ready Set seems to ignore that even if told to look for LINK records. The distance in the model is actually around 1.9 Ä and automatic ligand linking is on and set well below that distance. Any ideas why this might be failing and what is the smartest way to proceed? Any ideas highly appreciated. Thanks a lot Julian Esselborn Tezcan Lab UC San Diego

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Research Track Assistant Professor Positions
by Diana Tomchick 22 May '17

22 May '17

Assistant Professor, Research Track Department of Biophysics The Structural Biology Laboratory at UT Southwestern Medical Center currently has two openings at the non-tenure track Research Assistant Professor level for highly-motivated individuals who enjoy working in a collaborative, multi-disciplinary setting. · Position #1: Cryo-electron microscopist with extensive experience in high resolution single-particle reconstruction, including sample grid preparation, data collection, the use of modern software for particle picking and classification, map generation, model building and structure validation. Experience in cryo-EM tomography is a plus. · Position #2: X-ray crystallographer with extensive experience in modern methods of crystallization, data collection using home and synchrotron sources, structure solution via various experimental techniques, refinement and structure validation. For both positions, a Ph.D. in biochemistry, chemistry, physics or a related field is required. Facility with related techniques for each position such as cryo-electron microscopy, X-ray crystallography, NMR, small-angle X-ray scattering, isothermal titration calorimetry, analytical ultracentrifugation and protein expression and purification is highly desirable. Job requirements include a significant amount of both formal and informal teaching, and teaching experience is highly desirable. Salary is competitive and commensurate with experience and qualifications. About the UT Southwestern Structural Biology Laboratory The Structural Biology Laboratory (Diana Tomchick, Director) is a platform that allows researchers with different expertise to come together in a collaborative setting and tackle biological problems in a comprehensive way. Our publications are representative of the success of this strategy: http://www3.utsouthwestern.edu/sbl/Publications.html State-of-the-art equipment is currently installed, operational and shared between the members in the Structural Biology community at UT Southwestern. Cryo-EM equipment consists of one 300 kV Titan Krios microscope, one 200 kV Talos Arctica microscope, and a cryo-Scios DualBeam for cryo-FIB milling. In addition, the Structural Biology Laboratory has a dedicated lab for cryo-EM grid preparation, with an FEI Vitrobot and assorted instruments for sample prep. Computational facilities include a campus high-performance computing cluster. Crystallographic equipment includes an Art Robbins Gryphon crystallization robot and a Scorpion liquid handling robot, a Jansi UVEX UV microscope, a Rigaku FRE superbright rotating anode X-ray generator with an ACTOR sample mounting robot, and 30 days of guaranteed synchrotron beam time at Sector 19 of the Advanced Photon Source. These facilities are supplemented by a variety of biophysical instruments supporting the study of macromolecules using NMR, CD, dynamic light scattering, analytical ultracentrifugation, stopped-flow kinetics, isothermal titration calorimetry, microscale thermophoresis and mass spectrometry. Applicants should submit a curriculum vita and three letters of reference by July 10, 2017 to Diana Tomchick, Chair, Structural Biology Laboratory Search Committee, U.T. Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-8816. UT Southwestern is an Affirmative Action/Equal Opportunity Employer. Women, minorities, veterans and individuals with disabilities are encouraged to apply. For further inquiries, please contact: Diana Tomchick Department of Biophysics, Rm. ND10.214A UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390-8816 Tel. +1 214 645 6383 Email: Diana.Tomchick(a)UTSouthwestern.edu<mailto:[email protected]> ? ************************************************** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry University of Texas Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 Diana.Tomchick(a)UTSouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Amit D invited you to check out Dropbox
by Dropbox 20 May '17

20 May '17

Hi there, Amit D (amitd453(a)gmail.com) thinks you should use Dropbox! It’s a free and easy way to access and share your docs, photos, and videos with colleagues and friends—even if they don’t have Dropbox accounts. Accept invite[1] Get started through this email, and you’ll get an extra 500 MB added to your 2 GB of free space. Happy Dropboxing! [1]: https://www.dropbox.com/l/AADiCZMqlucm1Gb-DwLfoxb-Ub8mVCIREm0

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pdb help
by jp d 19 May '17

19 May '17

hi, phenix version 1.11.1-2575 FEM has crashed a few times for me . i have tried using various parameters (resolution_factor=1./3, use_resolve=False) , but it will max out my RAM (24G) and get into swap space. It gets very memory intensive, i think thats why it crashed. Do you have any suggestions to try ? i previously had a similar problem with a pdb using conflicting chain assignments, but this pdb doesn't use chains thanks jpd

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Electronic Laboratory Notebook
by Sebastiano Pasqualato 19 May '17

19 May '17

Dear all, another enquiry for the great community! We are considering the idea of moving to electronic laboratory notebooks rather than paper ones. Are you happily using one and would warmly suggest its implementation? Our department does not only deal with biochemical experiments, but performs a lot of genomics (big data analysis) and mouse genetics experiments, so experience of Notebooks used in departments that also have those activities would be a plus. We will consider free and paid softwares, if you have information on the costs that would be also very much appreciated! Thanks a lot, ciao Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEOXtalUnit

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Associate Researcher Position at the University of Kansas Protein Structure Laboratory
by Lovell, Scott W 17 May '17

17 May '17

The Protein Structure Laboratory at the University of Kansas is seeking a full-time Associate Researcher to assist with various structural biology projects. For a full description and to apply, GO TO: https://employment.ku.edu/staff/8691BR Review of applications begins 5/30/17 Regards, Scott __________________________________ Scott Lovell Ph.D., Director Protein Structure Laboratory University of Kansas Del Shankel Structural Biology Center 2034 Becker Drive Lawrence, KS 66047 Office: SBC 1015 Email: swlovell(a)ku.edu<mailto:[email protected]> Website: https://psf.cobre.ku.edu/cores/psl/about Phone: 785-864-3772 __________________________________

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kick maps
by jp d 12 May '17

12 May '17

hi, sorry if this is easily googleable, but i am not having any luck. how can i generate a kick map? thanks jpd

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Error running ERRASER
by Eric Montemayor 12 May '17

12 May '17

Has anybody encountered this error when running ERRASER in Phenix? If so, any suggestions for how to fix this would be greatly appreciated! -------------------------------------------------------------------------- *TypeError : ('__init__() takes at least 3 arguments (1 given)', <class 'subprocess.CalledProcessError'>, ())Traceback (most recent call last): File "/opt/sbgrid/i386-mac/phenix/1.11.1-2575/phenix-1.11.1-2575/modules/phenix/wxGUI2/App.py", line 784, in OnTimer self.run_manager.update(update_backgrounded=False) File "/opt/sbgrid/i386-mac/phenix/1.11.1-2575/phenix-1.11.1-2575/modules/phenix/wxGUI2/ProcessControl.py", line 213, in update process.update() File "/opt/sbgrid/i386-mac/phenix/1.11.1-2575/phenix-1.11.1-2575/modules/phenix/wxGUI2/ProcessControl.py", line 136, in update self._process.update() File "/opt/sbgrid/i386-mac/phenix/1.11.1-2575/phenix-1.11.1-2575/modules/cctbx_project/libtbx/runtime_utils.py", line 306, in update (error, traceback_info) = easy_pickle.load(self.error_file) File "/opt/sbgrid/i386-mac/phenix/1.11.1-2575/phenix-1.11.1-2575/modules/cctbx_project/libtbx/easy_pickle.py", line 82, in load return cPickle.loads(_open(file_name, "rb").read())TypeError: ('__init__() takes at least 3 arguments (1 given)', <class 'subprocess.CalledProcessError'>, ())* -------------------------------------------------------------------------- -- Eric J. Montemayor, Ph.D. Associate Scientist University of Wisconsin-Madison 145 Biochemistry Laboratories 433 Babcock Drive Madison, WI 53706 512.784.5981 http://about.me/montemayor https://www.linkedin.com/in/ericmontemayor <https://www.linkedin.com/pub/eric-montemayor/63/121/98b>

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ERRASER fails to run on ribosome model
by #AHMED TOFAYEL# 11 May '17

11 May '17

Dear PHENIX and ERRASER developers, While ERRASER is running fine (command line) when I use a small PDB file, it fails repeatedly on a complete ribosome model giving following error: Starting erraser Date: Tue May 9 17:53:20 2017 Directory: /home/tofayel/Desktop/test HOSTNAME: localhost.localdomain Log file will be /home/tofayel/Desktop/test/erraser.log Splitting output to /home/tofayel/Desktop/test/erraser.log Running ERRASER Rosetta app... ################################### Path to ERRASER: /usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER ERROR: Unique best command line context option match not found for -fixed_res. Possible matches include: -willmatch:fixed_res -stepwise:fixed_res -rna:farna:erraser:fixed_res Either specify namespace from command line; or in code, use add_relevant() to register option. Traceback (most recent call last): File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/erraser.py", line 14, in <module> erraser_run=phenix.erraser.erraser.erraser(args=sys.argv[1:]) File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/erraser/erraser.py", line 349, in __init__ self.run(params,out=out) File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/erraser/erraser.py", line 459, in run erraser(option) File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/erraser_wrapper.py", line 92, in erraser full_struct_slice_and_minimize( minimize_option ) File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/erraser_wrapper.py", line 662, in full_struct_slice_and_minimize erraser_minimize( minimize_option ) File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/erraser_wrapper.py", line 488, in erraser_minimize subprocess_call(command, sys.stdout, sys.stderr) File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/erraser_util.py", line 101, in subprocess_call subprocess.check_call(command, shell=True, stdout = out_channel, stderr = err_channel) File "/usr/local/phenix-1.11.1-2575/base/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '/usr/local/rosetta_src_2016.32.58837_bundle/main/source/bin/erraser_minimizer.linuxgccrelease -database /usr/local/rosetta_src_2016.32.58837_bundle/main/database/ -s /home/tofayel/Desktop/test/test-model-coot-19_erraser_temp/minimize_0_full_minimize_temp/before_min_temp_rs.pdb -score:weights stepwise/rna/rna_hires_elec_dens_FCC2012 -score:rna_torsion_potential FCC2012_RNA11_based_new -rna::corrected_geo true -rna::rna_prot_erraser false -rna::vary_geometry true -constrain_P true -attempt_pyrimidine_flip false -rna:farna:erraser:skip_minimize false -chemical:enlarge_H_lj false -in:guarantee_no_DNA false -scale_d 100 -scale_theta 10 -stepwise:rna:o2prime_legacy_mode true -use_2prime_OH_potential false -fixed_res 78 79 100 101 102 106 107 108 109 110 115 116 -edensity:mapfile /home/tofayel/Desktop/test/test-map.ccp4 -edensity:mapreso 3.3 -edensity:realign no -graphics false -skip_connect_info true ' returned non-zero exit status 255 Please suggest some fixes. Thanks in advanced. Best regards, Tofayel

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error when running the tutorials?
by Murpholino Peligro 10 May '17

10 May '17

[murphy@eva00 tut-phenix]$ phenix.run_example gene-5-mad Examples to be run: gene-5-mad Running PHENIX example: gene-5-mad Wed May 10 21:24:26 CDT 2017 Working directory: /home/murphy/X-Rays/tut-phenix/gene-5-mad Starting run now ... please wait a moment Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] Traceback (most recent call last): File "/home/murphy/X-Rays/phenix/phenix-dev-2747/build/../ modules/cctbx_project/site.py", line 48, in <module> import os ImportError: No module named os tutorial files look ok. ps running phenix dev2747 happens the same thing with p9-sad

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how to run Rosetta using phenix GUI interface on windows
by chen c 08 May '17

08 May '17

Hi, everyone, Can anybody tell how to run Rosetta using phenix GUI interface on windows system? Thank you so much! Best regards Chen -- Cheng Chen, Ph.D. Candidate Laboratory of Structural Biology Life Science Building,Tsinghua University Beijing 100084 China Tel:+86-10-62772291 Fax:+86-10-62773145 E-mail:[email protected] 北京市海淀区清华大学生命科学馆201-212室邮编：100084

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phenix real space refine & free R reflections
by Hillen, Hauke 05 May '17

05 May '17

Dear Phenix bb, I have a rather conceptual question regarding the treatment of free R flags in phenix.refine and phenix.real_space_refine. I am refining an xray structure using phenix.refine (but not using the real space refinement implemented there) and at some point decided to play a bit with the standalone program phenix.real_space_refine. In particular, I was interested in testing real space refinement against different maps (experimental map vs. model-phased). Being used to the excellent handling of free R flags in Phenix, I assumed giving phenix.real_space_refine the output MTZ of a previous phenix.refine run as a map would be safe to do. But I then saw the phenix.refine FAQ states the following: "Are R-free flagged reflections included in the maps used for real-space refinement? No, this is almost guaranteed to bias R-free; these reflections are removed internally prior to map calculation. However, the output maps will include these reflections unless you explicitly request otherwise.” While it makes sense to me that including the free reflections in the maps used for real space refinement will bias R-free, I wonder why the default behavior of phenix.refine is to output maps which include these reflections. I assume most users will use these output maps (for example via the OPEN IN COOT button in the GUI) to iteratively improve their model by local real space refinement in Coot. Conceptually, how is real space refinement performed by phenix.refine (where the free R reflections are not used to calculate the map to refine against) different from manual local real space refinement in Coot? Will the latter not also bias R-free when the default output maps from phenix.refine are used? Best, Hauke

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Different stats with different number of macrocycles
by Patrick Loll 05 May '17

05 May '17

Hi, I have an odd observation. I am finishing a refinement at 2.5 Å, using the Phenix GUI. I performed a three-macrocycle refinement, and saw that the geometry (RMS bonds/angles) and R/Rfree all got better in the first macrocycle, and then worsened in the subsequent two macrocycles. OK, fine. So I repeated the refinement, except I performed only a single macrocycle (starting from the exact same input coordinates). However, the statistics after this one-macrocycle job did not match the stats seen after 1 macrocycle in the 3-macrocycle job (?!). This doesn’t make sense to me; if you’re starting from the exact same coordinates, shouldn’t the first macrocycle always wind up at the same place, regardless of whether or not the program goes on to do additional macrocycles of refinement? In case this isn’t clear: In the 3-macrocycle job, after the first macrocycle, RMS bonds/angles = 0.005 Å/0.9 deg, R/Rfree = 0.208/0.236 (by the end of the third macrocycle, these numbers have changed to 0.009 Å/1.41 deg and 0.212/0.244) At the end of the 1-macrocycle job, RMS bonds/angles = 0.008 Å/1.4 deg, R/Rfree = 0.209/0.240 This is Phenix version 1.11.1-2575-000. Any insights welcome. Cheers, 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 pat.loll(a)drexelmed.edu

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Phenix Generate Table 1 Tool for twin-refinement statistics
by Xiao Lei 04 May '17

04 May '17

Dear All, I am using Windows Phenix Version 1.11.1. I'd like to generate table 1 for journal using Phenix "Generate Table 1 tool". In the input column, I input pdb model, data mtz, and data unmerged mtz, it gives me output statistics without twin refinement. But I'd like to show the results of twin refinement because I used Refmac5 to do twin refinement. Even I put the pdb from the output after twin refinement, the tool still gives me without twin refinement statistics. Thanks ahead for any input.

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TLS refinement
by Reza Khayat 02 May '17

02 May '17

Hi, I'm having difficulty with performing TLS refinement on a highly symmetric system. The difference between the R_work and R_free increases with TLS refinement (16.5/21.4 changes to 14.4/22.2). The TLS tensors for some of the group are not sensible (if I understand the literature correctly) -there are some negative numbers for the T and L tensors (see below). The TLS groups were identified with phenix.find_tls_groups. Any suggestions would be appreciated. REMARK 3 SELECTION: chain 'A' and (resid 38 through 68 ) REMARK 3 ORIGIN FOR THE GROUP (A): 56.6459 -23.5648 -59.0695 REMARK 3 T TENSOR REMARK 3 T11: 0.2105 T22: 0.2895 REMARK 3 T33: 0.0962 T12: 0.0829 REMARK 3 T13: 0.0473 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.0446 L22: 0.0120 REMARK 3 L33: 0.0096 L12: 0.0246 REMARK 3 L13: 0.0209 L23: 0.0106 REMARK 3 S TENSOR REMARK 3 S11: 0.0228 S12: -0.0268 S13: -0.0023 REMARK 3 S21: -0.0507 S22: 0.0526 S23: -0.0287 REMARK 3 S31: -0.0296 S32: -0.0137 S33: 0.0534? The data set is complete at 2.3Å resolution and there are no strange crystal phenotypes. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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starting model using phenix.map_to_model
by Chang Sun 01 May '17

01 May '17

Hi there, I am currently using the phenix.map_to_model for model building from a cryo EM electron density map. One thing I am wondering is whether the starting model should be aligned with the original map or the shifted map produced in the process? Because in my case, most of the starting model is not retained in the final "map_to_model.pdb". BTW, Dr Terwilliger, thanks for devoloping this wonderful tool! Thanks, Chang Postdoctoral Research Associate , Gennis Lab Department of Biochemistry, University of Illinois A306 CLSL 600 S. Goodwin Ave Urbana, IL 61801 Phone: 217-333-4939

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