- phenixbb - phenix-online.org

ligand - protein close contact
by Nikos Pinotsis 07 Jun '17

07 Jun '17

Dear all, I have a protein-ligand structure with several chains in the AU. After refinement one of the ligands forms a close contact 1.8A with the protein. For the rest of the protein-ligand chains the same interaction is as expected to 2.7-2.8 A forming an H-bond. I tried to adjust this ligand with coot but everytime I am getting back the same 1.8 A close contact. There is enough density for the ligand and I can even see that it can fit better to distance 2.4-2.5A H-bond with the protein Is there a way to constrain this distance to more than 2A? Should I fix the ligand atom that interacts? Unless I am missing something more fundamental. The ligand cif file is the default in phenix, the data set is a quite decent 2.3A. thanks in advance for any suggestions Nikos -- Dr. Nikos Pinotsis Institute of Structural and Molecular Biology Department of Biological Sciences, 3rd Floor, R313 Birkbeck College Malet Street London WC1E 7HX T: +44 (0)207 631 6827 F: +44 (0)207 631 6803 M: +44 (0)792 384 3593

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Composite omit map
by Sam Tang 05 Jun '17

05 Jun '17

Dear all Sorry for a very basic question about generating an omit map. I am trying to generate a SA-omit map for only my ligand but not the protein core of my complex. I presume I can use phenix.composite_omit_map GUI and specify my ligand chain in Atom Selection? All other parameters being the same, I notice that when I did not select any atom the whole structure was divided to 30-40 regions but when I selected my ligand chain it now divides into 89 regions. Is there a reason why and is there any advantage to manually adjust the number of omit regions? Many thanks and regards Sam Biochemistry Programme, School of Life Sciences, CUHK

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Fitting ligand with DM map?
by Sam Tang 03 Jun '17

03 Jun '17

Dear community I guess it may not be a standard practice but I wonder if anyone has tried to use a density modified map for ligand building. My situation is that I am trying to fit a single strand DNA ligand into an enzyme model. The dataset is at 3 Ang, P1 space, with overall completeness of only about 88%. MR was done by the apo-enzyme and the density for the first two-third of the ligand is very good and could easily be modelled. Towards the last one-third the density becomes much weaker so nucleotides cannot be easily put. This is the only dataset so far, so multi-crystal averaging / map averaging is not possible at this stage. NCS averaging is also not possible. We did try to sharpen map during refinement. I understand that DM is usually used to improve phase at the initial stage esp. with experimental phasing. With MR would you think density modification could produce a better map to aid the modelling of the last one-third ligand? Can I use the denmod.mtz directly for manual model building? Any input would be very much appreciated. Best Sam Biochemistry Programme, CUHK

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Questions on TLS output and more info on phenix.tls
by Michael Garavito 30 May '17

30 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 24 May '17

24 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 21 May '17

21 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 11 May '17

11 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 02 May '17

02 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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FSC curve between experimental cryo EM map and model
by #AHMED TOFAYEL# 29 Apr '17

29 Apr '17

Dear all, If I want to calculate FSC curve between experimental cryo EM map and model, what is the correct procedure to do so? I will explain what I have tried so far. Although I have variable local resolution in my map, according to FSC=0.143 criterion I have a 4 Ang map (say 1.mrc), I have used 'molmap' command in Chimera to generate a simulated map at 4 Ang. Then I used "vop resample" to take care of the pixel and box values ( then saved as 2.mrc). Thereafter, I have used "e2proc3d.py 1.mrc fsc.txt --calcfsc=2.mrc and plotted the fsc.txt file to get the curve. I am not sure if I am on the right track. My pixel size is 1.28. Best regards, Tofayel

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radiation damage-induced phasing (RIP) tutorial
by Murpholino Peligro 28 Apr '17

28 Apr '17

Hi lads... Do you know if there is a good tutorial for doing RIP somewhere on the internet? What programs can do RIP? -SHELX -AutoRickShaw -? Thanks

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Can I use PHENIX "Find NCS" tool to verify space group ?
by Alex Lee 23 Apr '17

23 Apr '17

Hi All, I have a protein/dna dataset (3A resolution) with space group (SG) ambiguity, it could be P32 with two copies of molecules (one copy of molecule composed of protein homodimer with asymmetric dsDNA) in asymmetric unit (ASU) or P3221 with one copy of molecule in ASU. Both SG can give me MR solutions and after Refmac P32 Rfree is around 31% while P3221 Rfree is around 34% (without any twin refine at this stage). Density maps from both SG makes sense and they are similar by eye inspection. Because of partial twinning of the dataset (estimation twin fraction alpha around 0.22) , which confuse programs of assigning the correct SG. Pointless and Xtriage suggests P6222, which we are sure it's not correct (based on performance on both MR, Refmac and biology sense that dsDNA is asymmetric, and if P6222 is true then based on Mathew coef. there will be a monomer protein with single strand ssDNA in ASU). Zanuda suggests SG P32 in both cases (input experimental data P32 or P3221 along with refined model). However, Zanuda may not work well in twin case. In short, the problem now is to choose one SG from P32 or P3221. There is one suggestion that try SG P32, as there are two copies of molecules in ASU in P32 group, try find the NCS operator in P32 and check if this operator is close to crystallographic symmetry operator or not, if it is, then SG is P3221, if it's not, then SG is P32. I did a few rounds of search in Internet, I found Phenix "Find NCS tool" and input PDB of my refined structures from both P32 and P3221. For both test, Find NCS tool did find NCS operator but in the end of the log file I see the same results as below: This NCS object does not contain point group symmetry This NCS object does not contain helical symmetry. I am asking: 1. does "This NCS object does not contain point group symmetry" from Find NCS tool mean that NCS operator in my PDB is not crystallographic symmetry operator? 2. Is there a tool in Phenix which can find the NCS operator and check if the NCS operator is close to crystallographic symmetry operator or not? Thanks ahead.

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Marching tomorrow?
by lbetts0508 . 22 Apr '17

22 Apr '17

Dear all, I am marching in DC tomorrow for continued support of our wonderful National Laboratories and funding that made resources like PHENIX possible. What a treasure these have been. Thank you for your support of structural biologists all these years and I hope for your continued success! Laurie Betts Chapel Hilll,NC

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Cannot compile rosetta interface Centos 7 with 1.11.1
by ludovic Pecqueur 21 Apr '17

21 Apr '17

Dear Phenix developers, I installed the latest phenix version today (1.11.1-2575) on Centos 7.2 I have rosetta_2016.13.58602 When I try to compile the rosetta interface (after exporting PHENIX_ROSETTA_PATH), compilation fails (see end of message for errors). When I compile the rosetta interface using phenix 1.11-2567, compilation goes to completion without errors. If you have any idea of the change between the two versions leading to this issue. Thank you for your help, Ludovic. ######################## Error message: Substituting phenix.python into build shell scripts update_options.sh update_ResidueType_enum_files.sh /usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/rosetta_src_2016.13.58602_bundle/main/source ~> phenix.python scons.py bin mode=release extras=python -j 8 scons: Reading SConscript files ... Running versioning script ... fatal: Not a git repository (or any parent up to mount point /usr/local) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). Done. (0.0 seconds) file ./options.dox being updated file ./full-options-list.md being updated Number of option files updated: 2 Total 3657 options. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed scons: done reading SConscript files. scons: Building targets ... g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/hybridization/CartesianSampler.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/hybridization/CartesianSampler.cc In file included from src/protocols/hybridization/CartesianSampler.cc:17:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/cryst/cryst_movers.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/cryst/cryst_movers.cc In file included from src/protocols/cryst/cryst_movers.cc:16:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. gcc -o build/external/release/linux/3.10/64/x86/gcc/4.8/python/libsqlite3.so -shared build/external/release/linux/3.10/64/x86/gcc/4.8/python/dbio/sqlite3/sqlite3.os -L/usr/lib -L/usr/local/lib -Lexternal/lib -lpython2.7 -ldl -lpthread -lutil g++ -o build/external/release/linux/3.10/64/x86/gcc/4.8/python/libcifparse.so -Wl,-rpath=/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/rosetta_src_2016.13.58602_bundle/main/source/build/external/release/linux/3.10/64/x86/gcc/4.8/python -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib -shared build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/BlockIO.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifDataInfo.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifExcept.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFileReadDef.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParentChild.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParserBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScannerBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifString.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DataInfo.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DicFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParserBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScannerBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Exceptions.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenCont.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenString.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ISTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ITTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_ptr_vector.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_vector.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ParentChild.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/RcsbFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/RcsbPlatform.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Serializer.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TableFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParser.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScanner.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParser.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScanner.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regcomp.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regerror.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regexec.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regfree.os -Lexternal/lib -Lbuild/external/release/linux/3.10/64/x86/gcc/4.8/python -Lexternal -L/usr/lib -L/usr/local/lib -lpython2.7 -ldl -lpthread -lutil g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/PhenixInterface.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/PhenixInterface.cc In file included from src/core/scoring/cryst/PhenixInterface.cc:15:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/XtalMLEnergy.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/XtalMLEnergy.cc In file included from src/core/scoring/cryst/XtalMLEnergy.cc:16:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/hybridization/CartesianSampler.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/cryst/cryst_movers.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/PhenixInterface.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/XtalMLEnergy.os] Error 1 scons: building terminated because of errors.

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Generate a map showing local agreement between map and model
by #AHMED TOFAYEL# 18 Apr '17

18 Apr '17

Dear developers and users, Is it possible to generate a map to show local agreement between cryo-EM map and the model generated using the same map? If I am not wrong, the supplementary figure S5 had accomplished the job (using Chimera), but I don't understand how to generate a similar figure for my project. Is it possible to do with phenix? http://emboj.embopress.org/content/28/6/755 Best regards, Tofayel NTU Singapore

4 4

UTMB Sealy Center for Structural Biology Symposium - May 6 - Register NOW
by Mark A. White 17 Apr '17

17 Apr '17

You and your colleagues are cordially invited to join us for the 22nd Annual Structural Biology Symposium to be held at Levin Hall on the University of Texas Medical Branch Campus on beautiful Galveston Island on Saturday, May 6, 2017. The meeting is organized by the Sealy Center for Structural Biology & Molecular Biophysics and co-sponsored by the Keck Center for Computational & Structural Biology. This year’s speakers include: James Chou, Ph.D., Harvard Medical School Rachelle Gaudet, Ph.D., Harvard University Petr Leiman, Ph.D., Univ. of Texas Medical Branch Daniela Nicastro, Ph.D., Univ. of Texas Southwestern Medical Center Brian Shoichet, Ph.D., Univ. California San Francisco School of Pharmacy Kylie Walters, Ph.D., Center for Cancer Research, National Cancer Institute To register or for more information, visit http://scsb.utmb.edu/symposium register: http://scsb.utmb.edu/symposium/2017/registration.asp

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Understanding Biology through Structure, Santa Fe May 13-17
by Terwilliger, Thomas Charles 14 Apr '17

14 Apr '17

Hi Colleagues! I hope you can come to our symposium on Understanding Biology through Structure in Santa Fe this May 13-17! The Symposium will emphasize interactions between junior and senior researchers. We hope that this will present a special opportunity for junior researchers to present posters and meet senior scientists, for senior researchers to meet the next generation of structural biologists, and for all to discuss science in an informal setting. You can see the full program at https://conferences.newmexicoconsortium.org/conferences/ubts_17/program Understanding Biology through Structure Santa Fe, NM May 13-17 2017 Speakers Nucleic acid and protein-nucleic acid complexes Jamie Cate, University of California, Berkeley Eva Nogales, University of California, Berkeley Jody Puglisi, Stanford University Leemor Joshua-Tor, Cold Spring Harbor Laboratory Tom Steitz, Yale University Shigeyuki Yokoyama, RIKEN Structural Biology of Cell Signaling Axel Brunger, Stanford University Sharon Campbell, University of North Carolina Yvonne Jones, Oxford University Dorothee Kern, Brandeis University Cynthia Wolberger, Johns Hopkins University Hao Wu, Harvard University Disease and Drug Discovery Lesa Beamer, University of Missouri Tom Blundell, University of Cambridge Elizabeth Goldsmith, UT Southwestern Medical Center Lynn Howell, University of Toronto Michael Rossmann, Purdue University Erica Ollmann Saphire, Scripps Institute Natalie Strynadka, University of British Columbia Ian Wilson, Scripps Institute Crystallographic Methods Wladek Minor, University of Virginia Randy Read, University of Cambridge Jane Richardson, Duke University Tom Terwilliger, Los Alamos National Laboratory Isabel Uson, Institute of Molecular Biology, Barcelona Nadia Zatsepin, University of Arizona Membrane Protein Structures Susan Buchanon, National Institutes of Health Wayne Hendrickson, Columbia University Robert Stroud, University of California, San Francisco Nieng Yan, Tsinghua University Protein folding and Design David Baker, University of Washington Ken Dill, Stony Brook University David Eisenberg, University of California, Los Angeles Susan Marqusee, University of California, Berkeley Tobin Sosnick, University of Chicago Understanding Enzyme Function Catherine Drennan, Massachusetts Institute of Technology Andrzej Joachimiak, Argonne National Laboratory Ci Ji Lim, University of Colorado, Boulder Ilme Schlichting, Max Planck Institute for Medical Research All the best, Tom T ?

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Deadline approaching: 10th CCP4/APS Crystallographic School in the USA
by Sanishvili, Ruslan 13 Apr '17

13 Apr '17

Dear Colleagues, The deadline for application to the annual CCP4/APS school in macromolecular crystallography: “From data collection to structure refinement and beyond” is in less than a week - April 19. Please read the thread below for basic information on the school. For all details, please visit http://www.ccp4.ac.uk/schools/APS-2017/index.php With regards, 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 ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Sanishvili, Ruslan [rsanishvili(a)anl.gov] Sent: Wednesday, February 01, 2017 2:54 PM To: phenixbb(a)phenix-online.org Subject: [phenixbb] 10th CCP4/APS Crystallographic School in the USA Dear Colleagues, We are pleased to announce the 10th annual CCP4 crystallographic school “>From data collection to structure refinement and beyond”, held at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2017/index.php Dates: June 19 through 26, 2017 Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises Data collection workshop: 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 http://www.ccp4.ac.uk/schools/APS-school/publications.php 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 19. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2017/index.php Registration 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, lodging and breakfast. 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

1 0

8th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 13 Apr '17

13 Apr '17

Second announcement 8th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 5 - June 9, 2017 Detailed information can be found on the workshop web page: https://conference.sns.gov/event/66/ Application deadline: April 22, 2017 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome - however the course organization is not able to support travel or accommodation. The number of participants will be limited to 15. There is no registration fee for all selected participants. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (for graduate students only; 1/2 to 1 page), should be sent electronically to meilleurf(a)ornl.gov<mailto:[email protected]> before April 22, 2017. Flora Meilleur, Ph. D Associate Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

1 1

Refinement of two co-factors at the same position
by Kornelius Zeth 12 Apr '17

12 Apr '17

Dear all, I'm trying to refine the occupancy and position of two co-factors iron (III) and FEO (Fe-O-Fe) in a crystal structure. The iron (III) is placed with some occupancy on one of the iron positions in FEO. If I refine them together in Phenix with low occ phenix.refine moves the atoms apart. What is the best way of dealing with this problem? Thanks and best wishes Kornelius

2 1

Symposium on Understanding Biology through Structure, May 13-17, 2017, Santa Fe
by Wladek Minor 12 Apr '17

12 Apr '17

Dear Colleagues, As a member of the organizing committee of "Understanding Biology through Structure", I'd like to encourage you to come to Santa Fe May 13-17 to attend this exciting Symposium. In addition to an exceptional set of talks including X-ray crystallography, cryo-EM, biochemical and biophysical methods, the Symposium will emphasize interactions between junior and senior researchers. We hope that this will present a special opportunity for junior researchers to present posters and meet senior scientists, for senior researchers to meet the next generation of structural biologists, and for all to discuss science in an informal setting. The meeting website is at https://conferences.newmexicoconsortium.org/conferences/ubts_17 and the program can be seen at https://conferences.newmexicoconsortium.org/conferences/ubts_17/program Looking forward to seeing you there, Wladek Minor -- Dr. Wladek Minor Harrison Distinguished Professor Department of Molecular Physiology and Biological Physics Phone: 434-243-6865 Fax: 434-243-2981 http://krzys.med.virginia.edu/CrystUVa/wladek.htm US-mail address: Department of Molecular Physiology and Biological Physics University of Virginia PO Box 800736, Charlottesville, VA 22908-0736 Fed-Ex address: Department of Molecular Physiology and Biological Physics 1340 Jefferson Park Avenue University of Virginia Charlottesville, VA 22908 ----

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Fwd: [ccp4bb] Join the editorial team of IUCr Journals
by Randy Read 07 Apr '17

07 Apr '17

Just in case anyone on the Phenix BB doesn't read the CCP4 one! Best wishes, Randy Read > Begin forwarded message: > > From: Louise Jones <lj(a)IUCR.ORG> > Subject: [ccp4bb] Join the editorial team of IUCr Journals > Date: 7 April 2017 at 13:23:42 BST > To: CCP4BB(a)JISCMAIL.AC.UK > Reply-To: Louise Jones <lj(a)IUCR.ORG> > > Dear All > > We are now seeking a number of new Editors and Co-editors for IUCr Journals, including our biological journals > > > > Acta Crystallographica Section D, Structural Biology > and > Acta Crystallographica Section F, Structural Biology Communications > > Full details are available at > http://www.iucr.org/news/notices/announcements/chesternotice_2017_04 > > Best wishes > Louise > _____________________________________________________ > > Louise Jones > Managing Editor > Acta Cryst. D and Acta Cryst. F > International Union of Crystallography > ________________________________________________________ ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

1 0

New Phenix tutorial videos
by Dorothee Liebschner 07 Apr '17

07 Apr '17

Dear Phenix users, We uploaded more videos to the Phenix Tutorial YouTube channel <https://www.youtube.com/channel/UCcdI0hfHngWAZLJWynxPQWg>: - Basic Phenix eLBOW tutorial - How to run Phaser-MR from the Phenix GUI - Explaining the atom selection syntax To give us feedback, write to tutorials(a)phenix-online.org or use the comment section in YouTube. If you are eager to see a tutorial about a certain (Phenix-related) topic, don't hesitate to tell us. Further info: To see subtitles, hit the cc (closed captions) button in the right bottom of the video screen. Subscribe to the channel to see the tutorial videos in your YouTube subscription feed. To get notifications about new videos, tap the bell button (next to the "subscribe" button). Best wishes, The Phenix team

1 0

What happened with Rfree between dev-2376 and now?
by Mark Saper 29 Mar '17

29 Mar '17

Hi all, I’ve been running some tests with the current dev and released versions of Phenix. If I run the same job (same input files, same parameters), the current versions consistently result in Rfree values ~1% more than Phenix version dev-2376! What changed between then and now? 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

1 0

Note that R-free numbers are different than a year ago.
by Mark Saper 26 Mar '17

26 Mar '17

In July 2016, I finished a refinement with Phenix dev-2376 with these final stats start final --------------------------------------- R-work: 0.1982 0.2007 R-free: 0.2376 0.2367 RMS(angles): 0.55 0.45 RMS(bonds): 0.003 0.002 Today, I reran the exact same parameter file and input files with Phenix dev-2712: start final --------------------------------------- R-work: 0.2073 0.2037 R-free: 0.2445 0.2442 RMS(angles): 0.55 0.45 RMS(bonds): 0.003 0.002 R-free values are now higher than they used to be. This fact was also flagged when I ran Table 1 today. -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

1 0

help with pdbtools
by Edward A. Berry 25 Mar '17

25 Mar '17

1. I'm trying to use pdbtools and I don't quite get the syntax. How can I specify the output file name on the command line? these don't work: phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 output file_name = shake1.pdb phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 file_name = shake1.pdb phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 --output file_name = shake1.pdb phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 --file_name = shake1.pdb phenix.pdbtools --output file_name = shake1.pdb 2chr_refine_001.pdb sites.shake=0.5 phenix.pdbtools output.file_name = shake1.pdb 2chr_refine_001.pdb sites.shake=0.5 2. for the "shake" operation, is there a random seed so that it comes out differently each time? (If I do this five times with different output file names, will they all be the different?)

3 6

DNA double helix through crystal symmetry
by wtempel 25 Mar '17

25 Mar '17

Hello, how could one restrain DNA base pairing across a crystallographic axis? Are secondary_structure.nucleic_acid restraints "symmetry-aware"? Thank you. Wolfram Tempel

3 3

Berkeley Server Downtime (3/23 - 3/24)
by Billy Poon 24 Mar '17

24 Mar '17

Dear all, On Thursday, March 23, our servers will be shut down starting at 5:00 pm Pacific for some emergency electrical work near our building. We expect that the servers will be available the next day (3/24) by 1:00 pm Pacific. There is a possibility that the outage will last longer. This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience and the short notice. -- 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 1

options in phenix.merging_statistics
by Murpholino Peligro 24 Mar '17

24 Mar '17

Hello. I was wondering what is the normal situation where one should click the boxes marked as "Keep anomalous pairs separate in merging statistics" (option1) and/or "Use internal variance of the data in the calculation of the merged sigmas" (option2)? I am asking because it looks like it is detrimental to the statistics, as you can see in the file attached (CSV file with 4 columns for no options, option1, option2 and option1&2). Thanks in advance. MP

2 1

phenix ensemble ref.
by Kajander, Tommi A 23 Mar '17

23 Mar '17

Hi, is it possible to do ensemble refinement in phenix with just one domain? (and e.g. fix the other) Doens seem so? Thanks, Tommi

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Re: [phenixbb] Error running phenix.rosetta_refine tests with Rosetta 3.8
by Nigel Moriarty 21 Mar '17

21 Mar '17

Oliver My Rosetta 3.7 is 2016.32. Not sure why we are different. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Tue, Mar 21, 2017 at 8:19 AM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > Hi Nigel, > > I tried with rosetta 3.7 (2016.46) and phenix dev-2719, and this time > compilation using rosetta.build_phenix_interface was successful (scons > finished building targets with no errors), but when I run rosetta.run_tests > it still crashes, though with a different error (see attached log). Any > ideas as to how to fix? > > Cheers > Oli > > > > On Mar 20, 2017, at 7:31 PM, Nigel Moriarty <nwmoriarty(a)lbl.gov> wrote: > > Oliver > > We are currently only supporting up to Rosetta 3.7 as a c++11 compiler is > required for any subsequent versions. We have compiled using a c++11 > compiler with no problems so I suggest you revert to 3.7 or check the logs > for compilation problems. > > Cheers > > Nigel > > --- > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 <(510)%20486-5709> Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 <(510)%20486-5909> Web : CCI.LBL.gov > <http://cci.lbl.gov/> > > On Mon, Mar 20, 2017 at 9:34 AM, Oliver Clarke <olibclarke(a)gmail.com> > wrote: > >> Hi, >> >> Phenix rosetta refinement worked with previous versions of rosetta and >> phenix, but with the latest Rosetta version (3.8) and latest phenix nightly >> I get a crash when running rosetta.run_tests after building the rosetta >> phenix interface, which runs a test run of phenix.rosetta_refine. It gets >> to the stage of generating initial models and then crashes - see attached >> log. Ideas for a fix welcome! >> >> Cheers >> Oli >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > > > >

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Error running phenix.rosetta_refine tests with Rosetta 3.8
by Oliver Clarke 21 Mar '17

21 Mar '17

Hi, Phenix rosetta refinement worked with previous versions of rosetta and phenix, but with the latest Rosetta version (3.8) and latest phenix nightly I get a crash when running rosetta.run_tests after building the rosetta phenix interface, which runs a test run of phenix.rosetta_refine. It gets to the stage of generating initial models and then crashes - see attached log. Ideas for a fix welcome! Cheers Oli

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difference map for cryo-EM (cryo-EM map minus model map)
by Pavel Afonine 16 Mar '17

16 Mar '17

For those practicing cryo-EM and tending to use Phenix nightly builds, as well as in response to a recent post (Re: [phenixbb] difference map based on the cryo-EM map): Next Phenix nightly build (dev-2612 and up) will have a command line tool to compute map-model real-space difference maps. One map is computed in real space: cryo-EM map minus model calculated map; it is locally scaled in some complex way to account for local variations and possibly poorly refined B-factors. In terms of reciprocal space it is an analog of: (F_obs, Phase_obs) - (F_calc, Phase_calc). The other map is computed using both spaces, and is analog of (F_obs-F_calc, Phase_obs); here no model phase is involved. I'm not sure which one of the two is better. Both maps are useful to locate ligands or yet not built pieces of the model (very much like in crystallography). Current limitations: - no GUI; - map must have origin at (0,0,0); - output file name can't be changed. To use: phenix.real_space_diff_map model.pdb map.ccp4 resolution=3.9 which will output two maps: map_model_difference_1.ccp4 and map_model_difference_2.ccp4 . If proving ligand is the purpose to compute this map, then obviously it should not be present in model.pdb. In future (once fully tested) this will be integrated into phenix.real_space_refine. The tool is 10 hours old and tested on just one model (5l4g, emd_4002.map), so bugs are not unexpected. Any feedback is welcome! All the best, Pavel

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Re: [phenixbb] phenix.erraser and PHENIX_ROSETTA_PATH; problem fixed.
by Mooers, Blaine H.M. (HSC) 16 Mar '17

16 Mar '17

Hi Andy, Thank you for the clarification! Yes, I was wrong. There is still a tools subdirectory at the top level. I installed the latest version of Rosetta from source. This is version 3.8, the Feb. 25th, 2017 release. The rosetta\_options.py file is in the same location: main/source/src/apps/public/ERRASER. Following up on your suggestion, I edited the file erraser.py in /Applications/phenix-dev-2686/modules/phenix/phenix/erraser by replacing line 543 with the following: file_path = os.path.join(params.directories.rosetta_path, 'main/source/src/apps/public/ERRASER') Phenix.erraser now runs. Best regards, Blaine Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology, College of Medicine University of Oklahoma Health Sciences Center 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Faculty webpage<http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/…> X-ray lab (LBSF)<http://http://research.ouhsc.edu/CoreFacilities/LaboratoryofBiomolecularStr…> Molecular Graphics<https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/mo…> Links <https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/Mo…> Small Angle Scattering <http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/sma…> office: (405) 271-8300 lab: (405) 271-8313 e-mail: blaine-mooers(a)ouhsc.edu ________________________________ From: Andy Watkins [andy.watkins2(a)gmail.com] Sent: Tuesday, March 14, 2017 11:53 AM To: Mooers, Blaine H.M. (HSC) Subject: Re: [phenixbb] phenix.erraser and PHENIX_ROSETTA_PATH Yes, while the tools directory should still exist, the new path to ERRASER is in fact main/source/src/apps/public. I wonder if the issue lies in Phenix's subsequent interpretation of that environment variable -- i.e., the Phenix code is appending "tools/ERRASER" instead of the aforementioned path. On Mar 14, 2017 9:18 AM, "Mooers, Blaine H.M. (HSC)" <Blaine-Mooers(a)ouhsc.edu<mailto:[email protected]>> wrote: Dear phenixbb, This is a question about phenix.erraser. I had it running in March 2016, but it no longer works. I am using phenix-dev2686. I am also using the rosetta_src_2016.59086_bundle that was released in November 2016. Rosetta works fine for other tasks. I set in my bashrc file the following: export PHENIX_ROSETTA_PATH=/Users/blaine-mooers/software/rosetta_src_2016.46.59086_bundle If I use the gui or the command line, I get an error message that suggests using a relative path to the rosetta directory. This does not work either. I also tried extending the path incrementally down to the directory containing the erraser binaries. There must be some other issue. I suspect that between March and November 2016 that there has been reorganization of the directory hierarchy in rosetta. There is no longer a "tools" subfolder in the top directory. The file erraser_option.py is now located in ./rosetta_src_2016.46.59086_bundle/main/source/src/apps/public/ERRASER. Best regards, Blaine Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology, College of Medicine University of Oklahoma Health Sciences Center 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Faculty webpage<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.oumedicine.com_depa…> X-ray lab (LBSF)<https://urldefense.proofpoint.com/v2/url?u=http-3A__http-3A__research.ouhsc…> Molecular Graphics<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.oumedicine.com_doc…> Links <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.oumedicine.com_doc…> Small Angle Scattering <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.oumedicine.com_docs…> office: (405) 271-8300<tel:(405)%20271-8300> lab: (405) 271-8313<tel:(405)%20271-8313> e-mail: blaine-mooers(a)ouhsc.edu<mailto:[email protected]> _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb<https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai…> Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]>

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phenix.erraser and PHENIX_ROSETTA_PATH
by Mooers, Blaine H.M. (HSC) 14 Mar '17

14 Mar '17

Dear phenixbb, This is a question about phenix.erraser. I had it running in March 2016, but it no longer works. I am using phenix-dev2686. I am also using the rosetta_src_2016.59086_bundle that was released in November 2016. Rosetta works fine for other tasks. I set in my bashrc file the following: export PHENIX_ROSETTA_PATH=/Users/blaine-mooers/software/rosetta_src_2016.46.59086_bundle If I use the gui or the command line, I get an error message that suggests using a relative path to the rosetta directory. This does not work either. I also tried extending the path incrementally down to the directory containing the erraser binaries. There must be some other issue. I suspect that between March and November 2016 that there has been reorganization of the directory hierarchy in rosetta. There is no longer a "tools" subfolder in the top directory. The file erraser_option.py is now located in ./rosetta_src_2016.46.59086_bundle/main/source/src/apps/public/ERRASER. Best regards, Blaine Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology, College of Medicine University of Oklahoma Health Sciences Center 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Faculty webpage<http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/…> X-ray lab (LBSF)<http://http://research.ouhsc.edu/CoreFacilities/LaboratoryofBiomolecularStr…> Molecular Graphics<https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/mo…> Links <https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/Mo…> Small Angle Scattering <http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/sma…> office: (405) 271-8300 lab: (405) 271-8313 e-mail: blaine-mooers(a)ouhsc.edu

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Open Postdoctoral Position at Oak Ridge National Laboratory
by Paul Adams 10 Mar '17

10 Mar '17

Dear Colleagues, on behalf of my colleagues I’d like to bring to your attention an open postdoctoral associate position at Oak Ridge National Laboratory (ORNL): Summary - To maximize the information obtained for diffraction experiments for structural biology, data processing methods need to be improved for marginal, weak data and also for reflection overlap. Methods will be developed that make use of knowledge about the atomic model to inform data processing methods so that reflections can be successfully deconvolved. A novel technique for full profile single crystal structure refinement will be developed. This work will be performed through a National Institutes of Health (NIH) funded consortium between ORNL and Lawrence Berkeley National Laboratory (LBNL) to develop a broad range of computational tools for macromolecular neutron crystallography. The aim of this consortium is to address the need for new computational tools and methods to deal with the increasing number of neutron macromolecular structures being determined and their increasing size and complexity. These tools will be developed in close collaboration with the PHENIX program, a NIH funded consortium between several groups. Interested candidates should visit: https://www.ornl.gov/careers Job Posting: Postdoctoral Research Associate - Computational Methods for Integrating Protein Crystallography Data / NB50615195 https://recruiting-internal.ornl.gov/sap/bc/erecruiting/posting_apply?param… -- 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 80, Room 247 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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Please attend a workshop on Measurement and Interpretation of Diffuse Scattering in X-Ray Diffraction for Macromolecular Crystallography
by Robert Sweet 08 Mar '17

08 Mar '17

Driven by recent advances in this field we will hold a workshop to discuss it. The workshop will be on Monday, May 15, 2017 at Brookhaven Nat'l Laboratory, and will be affiliated with the 2017 Users' Meeting for NSLS-II and the Center for Functional Nanomaterials. The current draft agenda is on-line here: http://usersmeeting.ps.bnl.gov/workshops/workshop.aspx?year=2017&id=136 Registration for the Workshop and Users' Meeting is here: http://usersmeeting.ps.bnl.gov/registration/?year=2017 A description of the workshop is below. The Organizers: Robert Sweet (NSLS-II, BNL), Michael Wall (LANL), Nozomi Ando (Princeton University), James S. Fraser (University of California, San Francisco), George N. Phillips, Jr. (Rice University) For answers to questions, please contact Wall: mewall(a)lanl.gov or Sweet: sweet(a)bnl.gov Description: X-ray diffraction from macromolecular crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering reflects the mean electron density in the unit cells of the crystal. The diffuse scattering arises from correlations in the variations of electron density that may occur from one unit cell to another, and therefore contains information about collective motions in proteins. A major focus of the workshop will be to provide a roadmap to the acquisition of reliable data by surveying measurement methods and discussing the increase in measurement accuracy enabled by improved detectors, experimental methods, and data integration. Missing from recent results is real information about the behavior of the molecules being studied that would guide the thinking of biochemists and biologists. To discuss these and their relative merits will be a second major focus of the workshop. The charge to this workshop will be to provide a roadmap to efforts that will provide the biological understanding we believe is hidden in the data. ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Deputy Director, LSBR: The Life Science and ^ (that's L Biomedical Technology Research Center at NSLS-II not 1) Photon Sciences and Biology Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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on tst_af_3.exe
by Smith Liu 08 Mar '17

08 Mar '17

Dear All, What is the function of tst_af_3.exe in Phenix? It was in category "array_family", and a antivirus software in my computer has killed it as trojan. Smith

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map_to_model space group symbol not recognized
by CPMAS Chen 06 Mar '17

06 Mar '17

Hi, All when I try to using map_to_model tool to optimize my model from low-resolution map, phenix.map_to_model refine_2.mtz seq_from_pdb.dat I got the following error, even though I did not provide ncs file, Space group symmetry written as NCS operators to ncs_from_symmetry.ncs_spec Traceback (most recent call last): File "/usr/local/phenix-1.11-2567/build/../modules/phenix/phenix/command_line/map_to_model.py", line 9, in <module> run(sys.argv[1:],out=sys.stdout) File "/usr/local/phenix-1.11-2567/modules/phenix/phenix/autosol/map_to_model.py", line 5729, in run tracking_data=run_segment_and_split_map(params,out=out) File "/usr/local/phenix-1.11-2567/modules/phenix/phenix/autosol/map_to_model.py", line 4931, in run_segment_and_split_map ncs_group_obj,remainder_ncs_group_obj,tracking_data=segment_map(args) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 5795, in run params,map_data,pdb_hierarchy,tracking_data=get_params(args,out=out) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 2055, in get_params params=get_params_from_args(args) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 2051, in get_params_from_args return command_line.work.extract() File "/usr/local/phenix-1.11-2567/modules/cctbx_project/libtbx/phil/__init__.py", line 1757, in extract value = object.extract(parent=result) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/libtbx/phil/__init__.py", line 1757, in extract value = object.extract(parent=result) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/libtbx/phil/__init__.py", line 1122, in extract return self._type_from_words()(self.words, master=self) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/iotbx/phil.py", line 40, in from_words return sgtbx.space_group_info(symbol=str(symbol)) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/sgtbx/__init__.py", line 97, in __init__ symbols = space_group_symbols(symbol) RuntimeError: cctbx Error: Space group symbol not recognized: <cctbx_sgtbx_ext.space_group object at 0x101836e20> Would this be a bug or I simply missed something? Thanks! Charles -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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