- phenixbb - phenix-online.org

does phenix refine fill in missing data?
by Ursula Schulze-Gahmen 23 Jun '17

23 Jun '17

I have very anisotropic data. I used the staraniso webserver to analyse and process my data which creates a final merged file with very incomplete data in the outer shells. If I use this data file in Phenix, what will happen? Will Phenix automatically fill in the unobserved data? If so, can I prevent it from doing so? I am importing the data with the reflection file editor and it seems the reflections are being filled in already at this stage. Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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Cif file recognition
by Joel Tyndall 22 Jun '17

22 Jun '17

Hi there, Having a few minor issues with my phenix setup on windows 10. I have the latest stable build Phenix1.11.1-2575. When introducing a new ligand that exists in the monomer library, Pheix complains it does not have the geometry restraints (cif file) - somehow it is not seeing its own library. How can I set up the cif library as default? Cheers Joel Joel Tyndall | BSc(Hons) PhD Associate Professor in Medicinal Chemistry School of Pharmacy | Te Kura Mātauraka Wai-whakaora University of Otago | Te Whare Wānanga o Otāgo PO Box 56 9054 Dunedin | Ōtepoti New Zealand | Aotearoa Ph: 64 3 479 7293 Skype: jtyndall Website | pharmacy.otago.ac.nz

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sculptor modifications
by Emilia C. Arturo (Emily) 21 Jun '17

21 Jun '17

Hello All, Is there a way to identify quickly the changes to a model that Sculptor has made? I am running the Phenix GUI to use Sculptor. I have read through the out-put log file, and understand (mostly) the sculpt protocol as it relates to the circumstances under which modifications to main chain or side chains are made, but it would be nice to see (in a list format, perhaps) what changes (if any...) were made. Regards, Emily. -- "Study as if you were going to live forever; live as if you were going to die tomorrow." - Maria Mitchell "I'm not afraid of storms for I'm learning to sail my ship." - Louisa May Alcott

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phenix.map_to_model input mtz file failure
by dancingdream＠163.com 19 Jun '17

19 Jun '17

Dear Phenix bb, I intend to build a initial model by phenix.map_to_model. And the command line is as follows: phenix.map_to_model_1.12rc0-2787 map_coeffs_file=../rep_dm.mtz map_coeffs_labels="'FP,SIGFP' 'PHIDM' 'FOMDM'" seq_file=../resolve.seq is_crystal=True use_sg_symmetry=True density_select=False truncate_at_d_min=True and the feedback like this: Sorry: No initial assignment made for map_coeffs. Labels used: FP,SIGFP PHIDM FOMDM. Available labels: ['PHIB', 'FOM', 'HLA,HLB,HLC,HLD', 'FP,SIGFP', 'PHIDM', 'FOMDM', 'FDM', 'HLADM,HLBDM,HLCDM,HLDDM'] NOTE: grouped labels like 'FP,SIGFP' must stay together, have commas, and have no spaces. If they come from an MTZ file, they must be in adjacent columns as well. Suggested labels to use: PHIDM FOMDM I try many other input format of map_coeffs_labels, such as map_coeffs_labels="FP,SIGFP PHIDM FOMDM" map_coeffs_labels=["FP,SIGFP PHIDM FOMDM"] ... ... but the result is the same. Dose anyone can tell me how to fix this problem? Thank a lot. -- Wei Ding P.O.Box 603 The Institute of Physics,Chinese Academy of Sciences Beijing,China 100190 Tel: +86-10-82649083 E-mail: dingwei(a)iphy.ac.cn

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Overall anisotropic ADP in phenix.real_space_refine?
by Oliver Clarke 18 Jun '17

18 Jun '17

Hi, I wonder in phenix.real_space_refine whether it may be worth adding refinement of a single overall anisotropic ADP to the model - or a single TLS group with modeled anisotropic ADPs - in order to model the effects of overall orientation errors (which affect resolution more substantially towards the periphery) and preferred orientation (which tends to give rise to anisotropic resolution across the volume). Maybe this would be helpful at least in generating a calculated map that is better for difference map calculation, for example? Cheers Oli

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real_space_refine questions
by Daniel Larsson 14 Jun '17

14 Jun '17

I'm have some questions about doing real space refinements using phenix.real_space_refine. I am refining a model for an intermediate-resolution (3.79 Å) cryo-EM map. As the starting point I use a model from a higher-resolution map (3.25 Å) of the same system in another conformation. My idea is to first do rigid body fitting of domains and then gradually relax constrains and restraints. - Is it possible to restrain the position of certain parts of the model (i.e. "freeze" them so that they move at all) to do focused refinement of subdomains or loops? - In the instructions it says that you can do both NCS constraints and restraints. How you do the latter? I can only do the former by default or by defining ncs_constraints=True and give a NCS definition file. - When I do a run with run=rigid_body, some rigid body groups move in to each other and overlap. Is there no collision detection using this algorithm? If I do a run=minimization_global, things work a bit better in this regard, but is not really what I want (at this stage). Am I doing something wrong? Here is the run command and the rigid body definition file: phenix.real_space_refine \ model.pdb \ map.ccp4 \ rigid.eff \ resolution=8.0 \ ncs_constraints=False \ rotamer_restraints=True \ ramachandran_restraints=True \ c_beta_restraints=True \ run=rigid_body \ macro_cycles=10 # rigid.eff: refinement { rigid_body { group = chain A and resseq 101:266 group = chain A and resseq 273:388 group = chain B and resseq 101:266 group = chain B and resseq 273:388 group = chain C and resseq 104:266 group = chain C and resseq 273:388 } } Regards, Daniel Larsson

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 13 Jun '17

13 Jun '17

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission for the July 2017 issue is 30 June 2017. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. 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

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preparing DL-Malic acid stock solution
by Sebastiano Pasqualato 08 Jun '17

08 Jun '17

Dear all, we’ve recently having trouble preparing a 3 M stock solution of DL-Malic Acid, pH 7 (which we had, so it’s doable!). When we reach pH 3 - 4 the solution turns milky white and does not goes back to a clear solution even when the pH is raised. Does anybody have any advice on how to get a clear solution? Has anyone gone through the same? Thanks in advance, 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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Re: [phenixbb] AutoSol invalid MTZ column_types error
by Terwilliger, Thomas Charles 08 Jun '17

08 Jun '17

Hi Mintu, I'm sorry about this problem! I should have fixed it already but missed this message from Phil Evans that he posted in January: "Columns N(+) and N(-), both of type I, are recent additions to the output file from Aimless. They are the number of observations merged into I(+) and I(-) respectively" AutoSol doesn't know about these columns and can accidentally guess that they are data. To get around this column, use a command like this to create a data file that does not contain the N(+) and N(-) columns: phenix.reflection_file_converter aimless.mtz --mtz=aimless_noN.mtz --label="I(+" ?where the --label=xxxx command specifies the first few characters of the columns you want to use as I+/I- data. Then use aimless_nonN.mtz instead of aimless.mtz as input to autosol. I will fix this in autosol. Let me know if that does not do it! All the best, Tom T Dear all, I am getting an error message "Invalid MTZ column_types for the given miller_array." while I try to run AutoSol. The last line in the log is "Adding array ['N(+)', 'N(-)'] to output file with type II". Do you have any suggestion how to fix this error? Thanks a lot in advance. Best, Mintu

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comfortable OS X level
by Patrick Loll 07 Jun '17

07 Jun '17

I’m still running Yosemite on my Macs, both because I’m change-averse and because folks reported problems with some crystallographic software upon upgrading the OS. These reports have now faded into the haze of the past, and so I ask, have the issues been resolved? Is it safe to move to Sierra? Thanks as always, 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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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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