- phenixbb - phenix-online.org

Re: [phenixbb] [cctbxbb] Update to allsvn script?
by Billy Poon 20 Oct '17

20 Oct '17

Hi all, Is anyone still using "allsvn" from the phenix_regression repository? If not, we'll just delete it next Friday (10/27) since it's hopelessly out of date. The functionality has been superseded by bootstrap.py. Thanks! -- 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 On Thu, Oct 19, 2017 at 11:22 PM, <Graeme.Winter(a)diamond.ac.uk> wrote: > Folks, > > phenix_regression/allsvn assumes if you are using git that you are using > git/svn > > These days probably not true ;o) > > Viz: > > > cd cctbx_project; git svn rebase > > Unable to determine upstream SVN information from working tree history > > > ccp4io: At revision 160. > > ccp4io_adaptbx: At revision 142. > > cd dials; git svn rebase > > Unable to determine upstream SVN information from working tree history > > someone on phenix-land want to have a look at this? Obviously not a > blocker but is untidy! > > Thanks Graeme > > > -- > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorised recipient of the > addressee please notify us of receipt by returning the e-mail and do not > use, copy, retain, distribute or disclose the information in or attached to > the e-mail. > Any opinions expressed within this e-mail are those of the individual and > not necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England > and Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

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Job opening: Postdoctoral Fellow in Structural Biology and Drug Discovery
by Schonbrunn, Ernst 19 Oct '17

19 Oct '17

Dear Madam/Sir, Please post the following open postdoctoral position on your job-board. Thank you, Ernst Schonbrunn ----------------------------------------------------------------------------------------------- Postdoctoral Fellow in Structural Biology and Drug Discovery Location: Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612 Department: Drug Discovery Department Job Details: Moffitt Cancer Center is internationally recognized for our focus on personalized cancer care and translational research. The mission of Moffitt is clear, focused, and fully stated in nine words, "To contribute to the prevention and cure of cancer." With a tradition of excellence that began with the first patient admission in 1986, dedicated Moffitt physicians, scientists, and staff members have remained committed to excellence in an atmosphere characterized by kindness, caring, and hope. The Schönbrunn lab studies the structure-function relationship of medicinally relevant proteins along with the discovery and development of novel small molecule inhibitors as therapeutics. We are involved in multiple projects working in team with medicinal chemists, biologists and clinicians on the targeting of proteins involved in cell signaling and epigenetic events. For an overview of our research approach and current projects please visit our web site at labpages2.moffitt.org/schonbrunn/<http://labpages2.moffitt.org/schonbrunn/>. Position Highlights: · We seek highly motivated postdoctoral researchers to work on inter-disciplinary projects towards the characterization and inhibitor development of diverse kinases and bromodomain-containing proteins. * The position provides exciting opportunities for biochemical, structural and cell-based studies of various drug-target interactions and rational drug design. The Ideal Candidate: · The ideal candidate has a Ph.D. degree in Biochemistry, Biology, Chemistry, Physics or related field and expertise in protein crystallography and biochemistry as demonstrated by publications in internationally recognized scientific journals. * Additional experience in cell biology is preferred. Responsibilities: · Candidates must be enthusiastic and dedicated to science with excellent organizational skills and effective at working independently, while also collaborating and assisting the team in its collective research goals. * Attention to detail and ability to work on multiple projects is required. * Excellent verbal and written communication skills are required. Credentials and Qualifications: * Ph.D. degree in Biochemistry, Biology, Chemistry, Physics or related field. A competitive salary and benefits package will be offered to the successful candidate. Interested applicants should send a single PDF file that includes a current CV with recent publications, a personal statement of scientific interests and goals (2-page maximum) and contact information for three references to Dr. Ernst Schönbrunn at Ernst.Schonbrunn(a)moffitt.org<mailto:[email protected]> Equal Employment Opportunity Moffitt Cancer Center is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, or protected veteran or disabled status. We seek candidates whose skills, and personal and professional experience, have prepared them to contribute to our commitment to diversity and excellence. [MOFFITT_2c_RGB for signature] Ernst Schönbrunn, PhD Associate Professor Moffitt Cancer Center 12902 Magnolia Drive, Tampa, FL 33612 | tel: 813-745-4703 | email: ernst.schonbrunn(a)moffitt.org Please consider the environment before printing this email. This transmission may be confidential or protected from disclosure and is only for review and use by the intended recipient. Access by anyone else is unauthorized. Any unauthorized reader is hereby notified that any review, use, dissemination, disclosure or copying of this information, or any act or omission taken in reliance on it, is prohibited and may be unlawful. If you received this transmission in error, please notify the sender immediately. Thank you.

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Install Phenix 2926 on Linux Fail
by Xiao Lei 18 Oct '17

18 Oct '17

Dear All, I was trying to install Phenix 2926 on Ubuntu Mate, after type sudo ./install I got the following fail message: ========================================================= Phenix Installation version: dev-2926 machine type: intel-linux-2.6-x86_64 OS version: 4.4.0-97-generic destination: /usr/local/phenix-dev-2926 # of processors: 4 ========================================================================= Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 275, in <module> installer(sys.argv[1:]).install() File "/home/linchenlab/Downloads/phenix-installer-dev-2926-intel-linux-2.6-centos5/lib/libtbx/auto_build/install_distribution.py", line 197, in install self.install_from_binary() File "/home/linchenlab/Downloads/phenix-installer-dev-2926-intel-linux-2.6-centos5/lib/libtbx/auto_build/install_distribution.py", line 319, in install_from_binary self.reconfigure(log=log) File "/home/linchenlab/Downloads/phenix-installer-dev-2926-intel-linux-2.6-centos5/lib/libtbx/auto_build/install_distribution.py", line 379, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/home/linchenlab/Downloads/phenix-installer-dev-2926-intel-linux-2.6-centos5/lib/libtbx/auto_build/installer_utils.py", line 81, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/usr/local/phenix-dev-2926/base/bin/python /usr/local/phenix-dev-2926/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/phenix-dev-2926/build --command_version_suffix dev-2926 phenix phaser solve_resolve labelit dials xia2 iota prime' failed with exit code 1 What I need to do to fix this?

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SHELX sites to use in Phenix.
by Mahmudul Hasan 18 Oct '17

18 Oct '17

Dear All, I am trying to solve a structure using Phenix with very low anomalous signal. After several trials it seems like the signal from Manganese is not enough to solve this protein structure. Reading information that SHELX is good in finding sites from low molecular weight molecules (e.g. S, etc.), I tried the online version of SHELX in CCP4 to find the sites. Now I would like use these sites found by SHELX to see if that help to solve the structure. My question is, what is the best way to include extra sites besides the program Autosol find itself? Your valuable suggestions will help me a lot to get going with my structure solution effort. Best wishes, Mahmudul Lund Sweden

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Model_vs_data speed
by Eric Williams 16 Oct '17

16 Oct '17

I'm having a devil of a time getting model_vs_data to run in a timely fashion. Running the latest stable Linux build on Ubuntu 14.04 takes on the order of 3 minutes per structure. That wouldn't be so bad if I weren't trying to run it on every entry in the PDB. Is it just a limitation of Python? SFCheck, which I think is written mostly in FORTRAN, runs in a few seconds. Any help anyone could offer would be appreciated. Thanks. :) Eric

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Re: [phenixbb] Small change in molprobity report on output pdb between dev-2873 and dev-2919?
by Christopher Williams 09 Oct '17

09 Oct '17

I'll take a look. Thanks for noticing! -Christopher Williams ---Richardson Lab On Mon, Oct 9, 2017 at 12:44 PM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > Hi Boaz, > > I had to disable it because it required re-calculation of all other > Molprobity metrics twice, which it time waste. > > @developers: Can someone from Richardson Lab fix this? > > Pavel > > > > On 10/9/17 09:35, Boaz Shaanan wrote: > > Hi, > > I noticed a small change in output pdb between these two versions in the > molprobity report (these are two different runs, so ignore the numerical > values)t: > > *dev-2919:* > > REMARK 3 REMARK 3 > REMARK 3 MOLPROBITY STATISTICS. > REMARK 3 ALL-ATOM CLASHSCORE : 3.13 > RAMACHANDRAN PLOT: > REMARK 3 OUTLIERS : 0.46 % > REMARK 3 ALLOWED : 3.24 % > REMARK 3 FAVORED : 96.30 % > > *dev-2873:* > > REMARK 3 MOLPROBITY STATISTICS. > REMARK 3 ALL-ATOM CLASHSCORE : 2.56 > REMARK 3 MOLPROBITY SCORE : 1.24 This line is missing from the > newer version > REMARK 3 RAMACHANDRAN PLOT: > REMARK 3 OUTLIERS : 0.46 % > REMARK 3 ALLOWED : 2.78 % > REMARK 3 FAVORED : 96.76 % > > I am just wondering whether this change is intentional. > > Cheers, > > Boaz > > > > > > > > > > *Boaz Shaanan, Ph.D. Dept. of Life > Sciences Ben-Gurion University of the > Negev Beer-Sheva > 84105 > Israel > E-mail: > bshaanan(a)bgu.ac.il <bshaanan(a)bgu.ac.il> Phone: 972-8-647-2220 Skype: > boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 * > > > > > > > > _______________________________________________ > phenixbb mailing [email protected]://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > > >

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Rosetta installation
by Daniele de Sanctis 08 Oct '17

08 Oct '17

Hi all I have some trouble installing rosetta. I followed the instruction as in https://www.phenix-online.org/documentation/reference/rosetta_install.html and everything went ok up to % rosetta.build_phenix_interface nproc=n but then % rosetta.run_tests fails with Rosetta command-line arguments: -parser:protocol /buffer/desancti/xtal/rosetta_src_2016.32.58837_bundle/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml -s 1yjp_rosetta_in.pdb -mtzfile 1yjp_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=1yjp_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -score:weights talaris2013_cart -nstruct 1 Generating 2 models on 1 processors... DEBUG dumping error message ERROR: Rosetta exited with status 139 stderr output: Segmentation fault (core dumped) Traceback (most recent call last): File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 305, in <module> run(sys.argv[1:], create_dir=True) File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run debug=params.output.debug) File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__ self.run_jobs() File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/modules/phenix/phenix/rosetta/refine.py", line 388, in run_jobs check_result(result) File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/modules/phenix/phenix/rosetta/refine.py", line 379, in check_result raise RuntimeError("Aborted due to error in job %d." % result.job_id) RuntimeError: Aborted due to error in job 1. Any idea? thanks Daniele

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Running Phaser with a already placed solution from a previous job
by vincent Chaptal 05 Oct '17

05 Oct '17

Dear everyone, this sounds trivial but I somehow can't make it work so I would appreciate any pointer. I have placed a component using phaser and would like to expand my search using this already placed component as partial solution. I open the full-featured interface of phaser in the GUI and select the box "Use partial solution from previous job" and select the job (nothing seems to happen there). I define my ensembles with ensemble_1 as "fixed partial solution" and ensemble_2 the one to search for. I then get the error message that "ense_1 from previous job is not specified on the current ensemble tab". Using the info button I see that "It is best to do this by modifying the configuration of the GUI from the previous Phaser run instead of starting from scratch, because the stored solutions do not contain the definitions of the search ensembles" but I don't understand what is asked for me to do here. When I restore the previous job, I can't see how I can start a new search from there. Any help would be greatly appreciated. Thanks Vincent I'm using phenix 1.12-2829. -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr

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map model correlations in real_space_refine
by Daniel Larsson 04 Oct '17

04 Oct '17

In version 1.12, what does the new map correlation numbers CC_mask, CC_volume and CC_peak in the log mean? How do they relate to the old "Map CC (whole unit cell)" and "Map CC (around atoms)" values (which in my opinion are more intuitive/descriptive and very useful numbers and I don't understand why they are no longer written to the log). Regards, Daniel

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help with phenix.ligand_identification
by Edward A. Berry 28 Sep '17

28 Sep '17

I'm having some problems using ligand_identification. I would like to restrict the search to a specific density peak, even if it is not the highest unmodeled peak or the highest Fo-Fc peak in the map. I tried using options: search_center="67.5 18.3 11.8" or ligand_near_res=S2063, Will the search be restricted to that region, or if a particuar ligand doesn't fit that blob, will it search through the rest of the map? If it is restricted, in what radius? Is this radius affected by the "search_dist" or "local_search" parameters? and local_search = True is default? Is there a threshold level for density level, below which building a ligand in a blob will not be attempted? I've tried with both search_center= and ligand_near_res=, and something gets built far away from that site. But there were errors, so I may have something wrong: phenix.ligand_identification mtz_in=sqr2803or13_031.mtz input_labels="2FOFCWT PH2FOFCWT" \ model=sqr2803or13_031.pdb ligand_near_res=S2063 nproc=2 After preparing the ligand library, then: Running LigandFit process 1... Number of atoms in ligand suc.pdb is 23 Running job sequence 1, ligand 2, in /tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_1... Evaluating all ligands in ligand-lib now...and placing fittedligand ### in resolve_ligand_###.pdb Number of atoms in ligand 2pe.pdb is 28 Running job sequence 0, ligand 1, in /tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_0... Process Process-2: Traceback (most recent call last): File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/sw/lnx/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/ligand_identification.py", line 1382, in RunLigandFit shutil.rmtree(ligandfit_dir) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 247, in rmtree rmtree(fullname, ignore_errors, onerror) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 256, in rmtree onerror(os.rmdir, path, sys.exc_info()) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 254, in rmtree os.rmdir(path) OSError: [Errno 39] Directory not empty: '/tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_1/LigandFit_run_1_/TEMP0' Process Process-1: Traceback (most recent call last): File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/sw/lnx/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/ligand_identification.py", line 1382, in RunLigandFit shutil.rmtree(ligandfit_dir) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 247, in rmtree rmtree(fullname, ignore_errors, onerror) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 256, in rmtree onerror(os.rmdir, path, sys.exc_info()) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 254, in rmtree os.rmdir(path) OSError: [Errno 39] Directory not empty: '/tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_0/LigandFit_run_1_/TEMP0' Evaluating LigandFit results ... The run continues, but it does not test any more ligands after those first two but goes on to evaluate the results. With nproc = 1, only 1 ligand gets tested. In all cases the first ligand in the library (2PE.pdb) is evaluated as the best. It is placed in density, but density that has already been built out with (and looks more like) a string of water molecules. And this is far from the selected residue or coordinates specified. The directory that raised the error when attempting to be deleted does eventually get removed: after the run there is no TEMP_N in the parent directory. Any suggestions would be welcome. Ed P.S. - running with .eff file: ['--show_defaults'] ligand_identification { mtz_in = sqr2803or13_031.mtz mtz_type = *F diffmap model = sqr2803or13_031.pdb ncpu = 1 n_indiv_tries_min = 30 n_indiv_tries_max = 300 n_group_search = 4 search_dist = 10 local_search = True search_center = "67.5 18.3 11.8" # ligand_near_res = S2063 verbose = False debug = False use_ligandfit = True search_mode = *default LigandFit temp_dir = Auto dry_run = False # number_of_ligands = 1 cc_min = 0.75 open_in_coot = False non_bonded = True keep_all_files = False # cif_def_file_list = real_space_target_weight = 10 # job_title = None ligandfit { } } gives: [['2pe.pdb', 'suc.pdb', . . . 'upl.pdb']] /tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2 ******************************************************************************* Sorry, the protein model file None does not seem to exist? ******************************************************************************* Running LigandFit process 0... Process Process-1: Traceback (most recent call last): File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/sw/lnx/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/ligand_identification.py", line 1122, in RunLigandFit shutil.copyfile(mtz_in,data_local) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 82, in copyfile with open(src, 'rb') as fsrc: IOError: [Errno 2] No such file or directory: 'None' Evaluating LigandFit results ... Lig_seq Placed/total cc_all cc cc_adj score Code HBscore Cannot find overall_ligand_scores.log0. This could mean that none of that (sub)set of ligand fitted well. None of the ligand fit the difference desity well enough. Please try the following -- 1) if you input a custom library, try to use the default library (no extra keywords needed), or 2) if you used the default library already, ususlly this means that the density is too small (> 6 atome or more is needed.) Exiting ...... No good ligand found.

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