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Using experimental phases in refinement
by Joseph Noel 26 Oct '13

26 Oct '13

Hi Folks, I am wondering if anyone can recommend some good reference(s) of structure refinements that employed experimental phases. We are attempting to collect experimental phases for a series of structures for which we have refined the structure already. I assume we can easily use initial model phases (space group doesn't change) to locate anomalous scatters and calculate experimental phases from the elucidation of the heavy atom arrangement. Most of the structures range from 1.7 to 2.4 A resolution. Would also appreciate any advice on the most efficient and accurate set of steps to accomplish this. If anyone thinks that this will not add much to the refinement of these structures would also appreciate some critiques. The protein in question crystallizes with 68% solvent content and one monomer per assymetric unit. We are employing ensemble refinement as the protein in question displays local conformational changes depending on the type of ligand(s) bound and also pH and similar but distinct crystallization conditions. We are carrying this out on ~400 mutants to do a very large scale comparison. Sorry for the long email but since we want to try and understand even minor conformational changes I thought phased-refinement would be much more powerful then refining just against the Fs. Thanks again in advance, Joe ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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protein-ligand complex structure
by Wei Shi 26 Oct '13

26 Oct '13

Hi all, I am working on a structure of protein-ligand complex. Four ligands are placed for the dimer protein and the density for the two ligands of the first monomer is better than the density for the other two ligands of the second monomer. Ligand is moved to fit density better in Coot (and for two ligands of the first monomer, they fits the density almost perfectly), but after a refinement in phenix (default settings + NCS restraints + Secondary structural restraints + Optimize X-ray/stereochemistry weight +Optimize X-ray/ADP weight), some part of the ligand which fits density good before moved out of the density again...Besides, it always shows green density in Coot for the ligand region even in places where the ligand is in density... Any suggestions or ideas about how to fit the ligand better and why the density for ligands of the second monomer is worse than that for the first monomer and why the ligands would move out of density after refinement? Is it because the protein model is not good enough to get the ligand density good? There is a conformational change upon ligand binding, and I rebuilt some part of the protein manually, and the density for a region of about 30 residues is not very good, and I tried to mutate those to alanies and refine, but it didn't help me see the density better... Any suggestions or ideas on how to improve this protein-complex structural model? Thank you so much! The statistics for the current best model is as follows, and the resolution of the dataset is 2.8Å. start final ------------------------------ ---------------- R-work: 0.3359 0.2993 R-free: 0.3619 0.3558 RMS(angles): 1.03 1.55 RMS(bonds): 0.006 0.007 MolProbity validation Ramachandran outliers: 4.7% (Goal: < 0.2%) Ramachandran favored: 85.3% (Goal: > 98%) Rotamer outliers: 4.5% (Goal: 1%) C-beta outliers: 0 (Goal: 0) Clashscore: 7.43 Overall score: 2.56 Thank you so much! Best, Wei

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Diffraction pattern from structure factors
by Bala Venkatakrishnan 25 Oct '13

25 Oct '13

Hi Are there programs available to generate a diffraction pattern from structure factors? Purely for learning purposes. -- Bala -- Balasubramanian Venkatakrishnan, Ph.D. Post-doctoral Fellow Molecular and Cellular Biochemistry Dept. 212 S Hawthorne Dr Simon Hall Room 213 Bloomington, IN 47405-7003 Indiana University Tel.:(812) 856-1874

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DEN refinement using CC instead of Rfree
by Morten Grøftehauge 25 Oct '13

25 Oct '13

Hi guys, Is there any way to do a DEN refinement run where it looks for the best map-model CC instead of the best Rfree? Even more useful would be map-model CC of selected residues... Or can I run DEN refinement on only part of the structure? That should in theory be faster. And since the Rfree values for the correct parts of the structure would be then fixed then I should get rid of the problem of Phenix selecting the refinement weights that result in the structure most like the input structure. Does that make sense? Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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job numbers
by SD Y 24 Oct '13

24 Oct '13

Hi, I am using latest version of Phenix. Since last week, I noticed that that two jobs having same number (not always). So, I cant open the recent job in GUI, though I could see results in folder. Is there any fix for this? ThanksSDY

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autobuild mistake
by Heather L Condurso 23 Oct '13

23 Oct '13

So I was running autobuild on the command line with: phenix.autobuild data=data.mtz model=model.pdb rebuild_in_place=False acceptable_r=0.2 I have a model from another data set that is missing some loops and new data sets which I would like to use autobuild to see if the model can be extended. I am using 1.8.4-1496 on a mac with osx 10.6.8. I was an idiot and when looking in the directory to check out one of the RUN_FILE_#.log files, I accidentally clicked on the RUN_FILE executable which started another AutoBuild subprocess. Since then all the other subprocesses had finished, but overall run stalled at: Splitting work into 4 jobs and running with 1 processors using sh background=False in ./AutoBuild_run_6_/TEMP0 Final job will be run with sh with background=True Starting job 1...Log will be: ./AutoBuild_run_6_/TEMP0/RUN_FILE_8.log Starting job 2...Log will be: ./AutoBuild_run_6_/TEMP0/RUN_FILE_9.log Starting job 3...Log will be: ./AutoBuild_run_6_/TEMP0/RUN_FILE_10.log Starting job 4...Log will be: ./AutoBuild_run_6_/TEMP0/RUN_FILE_11.log And the combine and extend didn't happen. I saw a post about combining models from autobuild but it was for rebuild_in_place=True and the post mentioned that the models needed to have identical sequences for it to work. Is there a way to save my mistake without starting over? The run I had restarted had yielded Rs=999.9 so If there is a way to maybe combine just 3 of the 4 that may be helpful as well. Thanks, Heather Condurso condurso(a)bc.edu

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No working nightlies since 1.8.4-1496?
by Ben Eisenbraun 23 Oct '13

23 Oct '13

Hi All, I don't see any nightlies listed since then, and trolling the build pages, it looks like things are in a state of flux right now with quite a few broken builds. I don't actually care about the nightlies per se; I have a user that wants to try PHENIX with Rosetta refinement, and per an older thread, we need a Rosetta nightly release for that to work. Do we also need a PHENIX nightly? Or should 1.8.4 work for this purpose? Thanks. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

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Postdoctoral Position in Protein Biochemistry / X-ray Crystallography (funded by Cancer Research UK) at ICR
by Sebastian Guettler 22 Oct '13

22 Oct '13

Dear PHENIX Community, We are currently looking for a postdoctoral fellow to join our research programme on the regulation and functions of ADP-ribosyltransferases. Please see the job description for the position and instructions on how to apply below. Best wishes, Sebastian Post-doctoral Training Fellow: Protein Biochemistry / X-ray Crystallography (funded by Cancer Research UK) We seek to appoint a Post-doctoral Training Fellow to a new team led by Dr Sebastian Guettler in the Divisions of Structural and Cancer Biology. The post is funded by Cancer Research UK. The successful applicant will undertake biochemical, crystallographic and functional studies on members of the ADP-ribosyltransferase (or “PARP”) family of proteins and their regulators. Our goal is to gain insight into the control and cellular roles of these enzymes with a specific interest in ADP-ribosyltransferase-dependent signalling processes linked to cancer. Applicants should possess a PhD (or equivalent) in biochemistry or molecular biology. Experience with recombinant DNA techniques, high-quality protein expression and purification, protein characterisation (such as protein-protein interaction analyses and enzymology) as well as protein crystallography is essential. Experience in protein production in insect cells would be of advantage. Appointment will be on a Fixed Term Contract for 3 years in the first instance, with a starting salary in the range of £28,425 to £34,944 p.a. inclusive (based on previous post-doctoral experience). For further details and instructions on how to apply, please refer to our online vacancy and recruitment site at http://www.icr.ac.uk/jobsearch, quoting job reference number 1376940 for this position. Closing date: 22nd November 2013 While applications need to be placed via our online system, informal inquiries can be sent to Dr Sebastian Guettler at sebastian.guettler(a)icr.ac.uk<mailto:[email protected]>. Research in the Divisions of Structural and Cancer Biology focuses on the functional, biochemical, and structural characterisation of cellular processes relevant to cancer and cancer therapy. The Division of Structural Biology has managed facilities for protein crystallography (crystallisation robots, Bruker Microstar and CCD detector), cryo-electron microscopy (FEI Tecnai F20 and T12), and protein production with expertise in multi-subunit expression (insect cell, yeast and bacterial expression, including a 60-litre fermentor). The Division is also well equipped with instrumentation for biophysical analysis (e.g. ITC, fluorescence, multi-angle light scattering). The Division of Cancer Biology provides a state-of-the-art infrastructure for mammalian cell culture, imaging, mammalian genetics, chemical biology and proteomics. The Institute of Cancer Research (ICR) is one of the world’s most influential cancer research institutes. Our mission is to make the discoveries that defeat cancer. We have a long and distinguished history of research with a major impact on the outcome for cancer patients. Our unique partnership with The Royal Marsden NHS Foundation Trust (RMH) makes us the largest comprehensive cancer centre in Europe, performing high quality original basic research and translational studies. Under the leadership of Chief Executive Professor Alan Ashworth FRS, we are committed to attracting, developing and retaining the best minds in the world. The ICR was ranked as the UK’s top academic research centre in the 2008 Higher Education Funding Council Research Assessment Exercise. Based on our publication record, citations and impact we rank among the world’s leading cancer research centres. Sebastian Guettler, PhD | Team Leader The Institute of Cancer Research | 237 Fulham Road | London | SW3 6JB | United Kingdom Lab: room 6S8 | Office: room 6S23.2 T (office) +44-(0)20-7153-5122 | T (lab) x5180 | Fax x5457 | E sebastian.guettler(a)icr.ac.uk<mailto:[email protected]> W http://www.icr.ac.uk/research/team_leaders/Guettler_Sebastian/index.shtml<http://www.icr.ac.uk/> | Twitter @ICRnews<https://twitter.com/ICRnews> Making the discoveries that defeat cancer [cid:[email protected]] The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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Autobuild error
by Nora Cronin 21 Oct '13

21 Oct '13

Whilst running Autobuild SA omit map using 40 segments one OMIT region fail and the program quits. Error as follow: Can you help? Summary of output files for Solution 1 from rebuild cycle 2 --- Model (PDB file) --- pdb_file: /local/ncronin/phenix/APC4/Autobuild_20131018/AutoBuild_run_2_/TEMP0/AutoBuild_run_5_/overall_best.pdb --- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag --- refine_data: /local/ncronin/phenix/APC4/Autobuild_20131018/AutoBuild_run_2_/TEMP0/AutoBuild_run_5_/overall_best_refine_data.mtz AutoBuild_build_cycle AutoBuild Run 5 Fri Oct 18 13:30:32 2013 Ending these rebuild cycles as the limit is reached All done with build cycles in this region AutoBuild_set_up_build AutoBuild Run 5 Fri Oct 18 13:30:32 2013 Traceback (most recent call last): File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 989, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 2146, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 1832, in AutoBuild_set_up_build self.AutoBuild_finish_current_region() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 1909, in AutoBuild_finish_current_region self.AutoBuild_update_ncs() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 5567, in AutoBuild_update_ncs ],quiet=True,out=f) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/find_ncs.py", line 324, in __init__ self.read_ncs_as_file(params,out=out) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/find_ncs.py", line 511, in read_ncs_as_file quiet=self.quiet,log=null_out()) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/simple_ncs_from_pdb.py", line 546, in __init__ starting_residue_numbers) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/simple_ncs_from_pdb.py", line 1326, in find_invariant_groups minimum_size=min_size) File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 35, in __init__ minimum_size=minimum_size) File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 70, in process size, index = self.find_largest( matches, used ) File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 168, in find_largest max_size = flex.max( sizes ) RuntimeError: unidentifiable C++ exception Traceback (most recent call last): File "/common/app/phenix/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/autobuild.py", line 230, in <module> run_autobuild=run_autobuild(args=sys.argv[1:]) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/wizard_command_line.py", line 564, in __init__ self.RunWizard() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/wizard_command_line.py", line 1000, in RunWizard self.runWizard.run() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/wizard_command_line.py", line 137, in run self.Wizard.Run(info='script') File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 838, in Run self.DoNextMethod() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 1003, in DoNextMethod raise AssertionError, line AssertionError: Traceback (most recent call last): File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 989, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 2146, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 1832, in AutoBuild_set_up_build self.AutoBuild_finish_current_region() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 1909, in AutoBuild_finish_current_region self.AutoBuild_update_ncs() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 5567, in AutoBuild_update_ncs ],quiet=True,out=f) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/find_ncs.py", line 324, in __init__ self.read_ncs_as_file(params,out=out) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/find_ncs.py", line 511, in read_ncs_as_file quiet=self.quiet,log=null_out()) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/simple_ncs_from_pdb.py", line 546, in __init__ starting_residue_numbers) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/simple_ncs_from_pdb.py", line 1326, in find_invariant_groups minimum_size=min_size) File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 35, in __init__ minimum_size=minimum_size) File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 70, in process size, index = self.find_largest( matches, used ) File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 168, in find_largest max_size = flex.max( sizes ) RuntimeError: unidentifiable C++ exception Best regards Nora Dr N B Cronin X-Ray Laboratory Manager Tel. (+44) 020 7153 5445 Section of Structural Biology Fax. (+44) 020 7153 5456 Chester Beatty Laboratories mobile: (+44) 07787554059 The Institute of Cancer Research 237 Fulham Road London SW3 6JB The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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anisotropic refinement based on B values
by Yarrow Madrona 20 Oct '13

20 Oct '13

I'm sure that this has probably already been covered but I am having some problem finding out how to tell phenix to make a decision whether to refine isotropically or anisotropically based on B factor values. Is this something you can do with a python script? Thanks. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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