- phenixbb - phenix-online.org

Need help with atom selection for anisotropic refinement
by Dr. Mark Mayer 27 Oct '13

27 Oct '13

Hi, I'm trying to do a mixed individual isotropic anisotropic refinement b factor refinement and can't get my atom selections to be accepted by phenix.refine. For the atoms I want to do isotropic refinement I used optional (element H or element D or resname HOH or chain E or chain F or chain A or chain B) for the anisotropic selection I used chain A and chain B and not (element H or element D or resname HOH or chain E or chain F or chain A resseq 5:11 or chain A resseq 66:72 or chain A resseq 117:138 or chain A resseq 152:184 or chain A resseq 196:210 or chain A resseq 249:251 or chain B resseq 3:6 or chain B resseq 66:72 or chain B resseq 166:210 or chain B resseq 249:251) I've tried various combuinations, but so far all have given the error message: Selection string results in empty selection. Thanks for your help Mark --

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Alternative Conformation, Restraints
by Moritz Machelett 27 Oct '13

27 Oct '13

Hello everyone, I am in the final rounds of refining my protein at high resolution and currently trying to model an alternative conformation of a Chl /a/-phytol chain. I inserted a second phytol chain with coot - worked out well so far (alternate chain identifiers A and B for both phytol chains). After using phenix.refine, however, the occupancy of the second phytol chain was refined to 0. When splitting the whole Chl molecule the occupancy refines to sensible values (0.34 and 0.66). We would prefer to only model the phytol chain in alternate conformation as the macrocycle superpose perfectly. Any suggestions regarding the occupancy problem? Another issue concerns restraints. We tried to turn of specific nonbonded restraints and found a phenixbb message from 2007: http://www.phenix-online.org/pipermail/phenixbb/2007-September/011734.html Are there any news/updates on this matter? Any help appreciated! Thanks, Moritz -- Moritz M. Machelett Ruhr University Bochum Protein Crystallography, Department of Biophysics, ND04/396 44780 Bochum Tel: +49-(0)234/32-25754

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fem map
by nih\mayerm 27 Oct '13

27 Oct '13

Hi, I'm trying to make a fem amp using phenix-1.8.4-1496 using my refined structure and mtz with map coefficients as input: phenix.development.fem 3222_Glu_refine_78.mtz 3222_Glu_refine_78.pdb coot 0.7.0-1 fails to generate a map when fem.mtz is opened, either in auto or manual mode mtzdmp for fem.mtz gives: Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 NONE -37 35 0 100.00 -5.0 14.2 61.69 1.21 H H 2 NONE 0 101 0 100.00 38.0 38.0 61.69 1.21 H K 3 NONE 0 44 0 100.00 16.8 16.8 61.69 1.21 H L 4 NONE 0.0 1796.7 25825 84.81 84.67 84.67 31.87 1.21 F 2mFoDFc 5 NONE -180.0 180.0 25825 84.81 1.07 90.28 31.87 1.21 P PHI2mFoDFc 6 NONE 0.0 2750.2 0 100.00 144.76 144.76 61.69 1.21 F 2mFoDFc_FilSharp 7 NONE -180.0 180.0 0 100.00 1.26 90.34 61.69 1.21 P PHI2mFoDFc_FilSharp 8 NONE 0.2 24426.8 0 100.00 235.27 235.27 61.69 1.21 F KICK 9 NONE -180.0 180.0 0 100.00 0.02 89.63 61.69 1.21 P PHIKICK 10 NONE 0.2 9283.0 0 100.00 132.01 132.01 61.69 1.21 F FEM 11 NONE -180.0 180.0 0 100.00 0.23 90.34 61.69 1.21 P PHIFEM

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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 25 Oct '13

25 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

2 1

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

3 3

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

2 1

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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Re: [phenixbb] increasing NCS restraints
by Mark van Raaij 17 Oct '13

17 Oct '13

Oops, 1 vote for making phenixbb default reply to sender only.... Mark van Raaij <mjvanraaij(a)cnb.csic.es> wrote: >Dont worry about it, we are alli diots...even without commuting 4 hrs a day > >Yarrow Madrona <amadrona(a)uci.edu> wrote: > >>Hi Dale, >> >>That is right! And that is what I concluded yesterday yet I somehow forgot >>all that overnight. Starting a new job and commuting 4 hours a day has >>taken a toll on my brain. I am an idiot. >> >>-Yarrow >> >>> >>> I'm puzzled. Didn't you say that the translation of your ncs >>> two-fold was not equal to half the "a" cell edge? If it is not >>> a translation of 1/2 (in fractional coordinates) then it cannot >>> be a crystallographic symmetry element and your space group cannot >>> be P212121. Unless this condition is met, the similarity of your >>> molecules is unimportant. >>> >>> Dale Tronrud >>> >>> On 10/17/2013 12:48 PM, Yarrow Madrona wrote: >>>> I am doing restrained NCS refinement and would like to know how to set >>>> the >>>> target weight of the cartesian restraint in the command line? I also >>>> found >>>> a sigma value in the GUI. I read that I can decrease it in order to >>>> increase the NCS restraints. However, I have seen this under Torsional >>>> restraints. Does this also apply to cartesian restraints? >>>> >>>> I am doing this so that I can look at the differences in position and >>>> B-factors of two molecules in the ASU that I am trying to determine are >>>> related by a perfect or imperfect 2(1) screw axis. (I posted a question >>>> about this on the CCP4 bullitan board.) If the values between molecules >>>> are exactly the same then presumably the space group is actually P212121 >>>> with 1molecule in the asu instead of P21 with two molecules. I already >>>> know that the P21 dimer superimposes almost exactly on the P212121 >>>> monomer >>>> and it's symmetry mate. I just don't know how "perfectly" they align and >>>> I >>>> am hoping this approach will tell me. I hope this makes some sense. >>>> >>>> -Yarrow >>>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >>> >> >> >>-- >>Yarrow Madrona >> >>Graduate Student >>Molecular Biology and Biochemistry Dept. >>University of California, Irvine >>Natural Sciences I, Rm 2403 >>Irvine, CA 92697 >> >> >> >>_______________________________________________ >>phenixbb mailing list >>phenixbb(a)phenix-online.org >>http://phenix-online.org/mailman/listinfo/phenixbb >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb

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Re: [phenixbb] increasing NCS restraints
by Mark van Raaij 17 Oct '13

17 Oct '13

Dont worry about it, we are alli diots...even without commuting 4 hrs a day Yarrow Madrona <amadrona(a)uci.edu> wrote: >Hi Dale, > >That is right! And that is what I concluded yesterday yet I somehow forgot >all that overnight. Starting a new job and commuting 4 hours a day has >taken a toll on my brain. I am an idiot. > >-Yarrow > >> >> I'm puzzled. Didn't you say that the translation of your ncs >> two-fold was not equal to half the "a" cell edge? If it is not >> a translation of 1/2 (in fractional coordinates) then it cannot >> be a crystallographic symmetry element and your space group cannot >> be P212121. Unless this condition is met, the similarity of your >> molecules is unimportant. >> >> Dale Tronrud >> >> On 10/17/2013 12:48 PM, Yarrow Madrona wrote: >>> I am doing restrained NCS refinement and would like to know how to set >>> the >>> target weight of the cartesian restraint in the command line? I also >>> found >>> a sigma value in the GUI. I read that I can decrease it in order to >>> increase the NCS restraints. However, I have seen this under Torsional >>> restraints. Does this also apply to cartesian restraints? >>> >>> I am doing this so that I can look at the differences in position and >>> B-factors of two molecules in the ASU that I am trying to determine are >>> related by a perfect or imperfect 2(1) screw axis. (I posted a question >>> about this on the CCP4 bullitan board.) If the values between molecules >>> are exactly the same then presumably the space group is actually P212121 >>> with 1molecule in the asu instead of P21 with two molecules. I already >>> know that the P21 dimer superimposes almost exactly on the P212121 >>> monomer >>> and it's symmetry mate. I just don't know how "perfectly" they align and >>> I >>> am hoping this approach will tell me. I hope this makes some sense. >>> >>> -Yarrow >>> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> > > >-- >Yarrow Madrona > >Graduate Student >Molecular Biology and Biochemistry Dept. >University of California, Irvine >Natural Sciences I, Rm 2403 >Irvine, CA 92697 > > > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb

1 0

increasing NCS restraints
by Yarrow Madrona 17 Oct '13

17 Oct '13

I am doing restrained NCS refinement and would like to know how to set the target weight of the cartesian restraint in the command line? I also found a sigma value in the GUI. I read that I can decrease it in order to increase the NCS restraints. However, I have seen this under Torsional restraints. Does this also apply to cartesian restraints? I am doing this so that I can look at the differences in position and B-factors of two molecules in the ASU that I am trying to determine are related by a perfect or imperfect 2(1) screw axis. (I posted a question about this on the CCP4 bullitan board.) If the values between molecules are exactly the same then presumably the space group is actually P212121 with 1molecule in the asu instead of P21 with two molecules. I already know that the P21 dimer superimposes almost exactly on the P212121 monomer and it's symmetry mate. I just don't know how "perfectly" they align and I am hoping this approach will tell me. I hope this makes some sense. -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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Re: [phenixbb] Need help with atom selection for anisotropic refinement
by Nathaniel Echols 16 Oct '13

16 Oct '13

I think the problem is with the boolean logic ("and"/"or"). First, the isotropic: optional (element H or element D or resname HOH or chain E or chain F or > chain A or chain B) > This will be processed okay but it's going to select all atoms in chains A/B/E/F in addition to all H/D and waters, which probably isn't what you really want since the anisotropic selection includes chains A and B. I'm not sure what will actually happen here, but it's better not to rely on the atom selections being processed in a particular order (and better not to rely on the code automatically handling the problem of overlapping selections). chain A and chain B and not (element H or element D or resname HOH or chain > E or chain F or chain A resseq 5:11 or chain A resseq 66:72 or chain A > resseq 117:138 or chain A resseq 152:184 or chain A resseq 196:210 or chain > A resseq 249:251 or chain B resseq 3:6 or chain B resseq 66:72 or chain B > resseq 166:210 or chain B resseq 249:251) > The problem here is that you have specified that the atoms match "chain A and chain B", which is impossible. You probably want this: (chain A or chain B) and not (....) -Nat

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phenix.rosetta_refine
by Guenter Fritz 14 Oct '13

14 Oct '13

Dear Phenix developers, I am working on a 3.6 A structure and want to try the latest joint development of phenix and rosetta. Is there are kind of "how_to" available online? Some do's and don'ts? Best, Guenter

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Phenix on Ubuntu12.3
by Swastik Phulera 12 Oct '13

12 Oct '13

Dear All, I am setting up a computer with ubuntu(12.3) installed on it. running "uname -rm" gives me 3.8.0-31-generic x86_64. I am trying to install phenix on this machine, as recommended I downloaded the 64 bit kernel 2.3 (64bit fedora 3 ) command line installer. I then ran ./install and source the required file by: source /usr/local/phenix-1.8.4-1496/phenix_env.sh but some how phenix refuses to start, following is the error phenix Traceback (most recent call last): File "/usr/local/phenix-1.8.4-1496/build/intel-linux-2.6-x86_64/../../phenix/wxGUI2/command_line/main.py", line 22, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.8.4-1496/build/intel-linux-2.6-x86_64/../../phenix/wxGUI2/command_line/main.py", line 16, in run from wxGUI2 import App File "/usr/local/phenix-1.8.4-1496/phenix/wxGUI2/App.py", line 15, in <module> import wx File "/usr/local/phenix-1.8.4-1496/build/intel-linux-2.6-x86_64/base/lib/python2.7/site-packages/wx-2.8-gtk2-ansi/wx/__init__.py", line 45, in <module> from wx._core import * File "/usr/local/phenix-1.8.4-1496/build/intel-linux-2.6-x86_64/base/lib/python2.7/site-packages/wx-2.8-gtk2-ansi/wx/_core.py", line 4, in <module> import _core_ ImportError: libjpeg.so.62: cannot open shared object file: No such file or directory Any suggestions would be welcome. regards Swastik

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Re: [phenixbb] Problem in reducing R-factor
by Nathaniel Echols 11 Oct '13

11 Oct '13

On Fri, Oct 11, 2013 at 6:19 PM, Ryan Spencer <rspencer(a)uci.edu> wrote: > For high resolution structures, below 1.5 Å, is there a set of > rules > for best practices for refinement? > Not really rules that I'm aware of... just general guidelines, and not well-codified. I've wanted for a long time for us to write some sort of extensive how-to across all resolution ranges, but like everything else, this has to compete with writing code and "real" papers. As Pavel mentioned, these resolution limits are somewhat subjective depending on completeness, how aggressively you process the data, etc. But, a few basic suggestions: - you will probably not want to use real-space refinement after the first couple of rounds - start parameterizing conservatively, then get more aggressive as you near the end of refinement (if nothing else, it's faster this way) - don't use any restraints other than the default geometry restraints plus whatever custom bonds are required by the chemistry (e.g. prosthetic groups) - use hydrogens by the end of refinement, but riding only until you're at subatomic resolution - the automatic weighting is probably going to work great; weight optimization might help for the final round, but probably not necessary - below 1.5Å, try making non-water/non-hydrogen anisotropic (and compare to purely isotropic); below 1.2Å, you can start thinking about making all non-H/D anisotropic. (Also note that heavier atoms can become anisotropic even earlier, so in your case, refining individual anisotropic B-factors for iodine and TLS for everything else would be a reasonable alternative.) - you should probably be able to get rid of all geometry outliers, including clashes - but you may see real (correct) Ramachandran or rotamer outliers at this point - you're inevitably going to see more blobs in the difference map that you can't explain than usual. don't sweat it. - you should definitely see a fair number of alternate conformations - I don't know what is expected statistically but I'd say at least 10% of protein residues will have them - pay attention to waters with close contacts to oxygen - these may be sodium (or other) ions I've attached a few slides that give *very approximate* suggestions - basically just reframing what Pavel and others have said over the years. Although some of these are pretty clear-cut (e.g. you absolutely do not want to use a reference model), you will always need to experiment somewhat to find out what is best for *your* model and data. I think based on your R-factors and statistics that you're headed in the right direction. I'd try to get the clashscore as close to zero as possible, though. I've been toying with different parameters and found that the > weighting didn't make a huge difference, which is probably expected, with a > 1.3 Å dataset. Do stereochemical/ADP weights have any effect? > Do you mean weight optimization? I wouldn't expect it to make much difference. > For the particular data set I'm working with, I'm refining directly > against anomalous data, more specifically against 12 Iodines. Refining the > f' and f" has worked well, generating a beautiful density map. > Good idea. Also consider looking at the anomalous residual map (map_type=anom_residual), which may show weaker anomalous scatterers like chloride or sulfur. (It will be flattened around the iodines if you refine their f'' values.) Refining against the model with hydrogens increased the Rfree/Rwork > values by about 2 points. From what I've read previously I thought refining > hydrogens in a non-"riding" model was only valid below ~1.0 Å. > I'm not sure what you mean here. Did you use the riding model and it increased R-free? Or only when you let them refine individually? The default is now to switch to individual only at 0.9Å or less. > by a few points. For water, I assume that at this resolution there is a > combination of anisotropic (big banana looking density) and isotropic > waters > and that one cannot simply rely entirely on the water_update option. > Yes, at some point you will need to complete the waters yourself. Those bananas may not be simply anisotropic waters, but split sites. You may see other small ligands too. The twin law has worked great, usually dropping Rfree/Rwork values > by 5 points or so. > Just remember to be careful when interpreting the effect of twin law application - I think in this case it's probably quite reasonable, but at lower resolution and with a worse model it can be extremely deceptive. I apologize if any of this is common knowledge and shows my relative > inexperience when it comes to best practices for crystal refinement. > No need to apologize - it is all oral tradition anyways. It is much better to ask questions now than to do something blindly and regret it later. -Nat

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Problem in reducing R-factor
by Singh, Bishal 11 Oct '13

11 Oct '13

Hi all, I am solving a crystal structure at 1.3Å. Completeness of the data-set and Figure of merit at this resolution are 99.5% and 0.62 respectively. Structure has two molecules per asymmetric unit. I used TLS parameters and NCS restraints. WXC_scale and WXU_scale are 0.50 and 1.0 respectively. Rwork and Rfree are 18.09 and 19.62 respectively. I tried with reducing WXC_scale and WXU scale to 0.25 and 0.30 respectively but it did not help. Please suggest me if I need to change some parameters. I shall be grateful for your help. Thanking you, Bishal Singh Graduate student University of Heidelberg, Germany

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special positions Refinement crash
by Yarrow Madrona 11 Oct '13

11 Oct '13

Hello, I am trying to do a refinement and I get an error that I think means I have atoms on special positions. The refinement stops and gives the following output given below. Any help would be appreciated. I am not sure how to exactly determine which atoms are at special positions. Thank you. -Yarrow |-real space refinement (target=simple)---------------------------------------| | start: r_work=0.5500 r_free=0.5441 rmsd: bonds=0.019 angles= 1.68 weight= 50| | final: r_work=0.5309 r_free=0.5358 rmsd: bonds=0.029 angles= 2.45 weight= 80| | --------------------------------------------------------------------------- | ==================== Compute data/restraints target weights =================== Traceback (most recent call last): File "/usr/bin/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/command_line.py", line 159, in run call_back_handler=call_back_handler) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/driver.py", line 1593, in run reference_model_manager = self.reference_model_manager).result File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/strategies.py", line 171, in __init__ ion_placement_manager = ion_placement_manager) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py", line 87, in __init__ self.call(self.weight, "Compute data/restraints target weights") File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py", line 137, in call func(prefix = prefix) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py", line 302, in weight log = self.log) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weights.py", line 20, in run log = log) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py", line 368, in __init__ self.xyz_weights_result = self.xyz_weights() File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py", line 411, in xyz_weights log=self.log) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py", line 294, in __init__ verbose=0) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/memory_eraser.py", line 29, in shake_sites max_iterations = max_iterations)) File "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py", line 43, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/usr/bin/phenix-1.8.4-1496/cctbx_project/scitbx/lbfgs/__init__.py", line 259, in run log) File "/usr/bin/phenix-1.8.4-1496/cctbx_project/scitbx/lbfgs/__init__.py", line 127, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py", line 89, in compute_functional_and_gradients self.apply_shifts() File "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py", line 70, in apply_shifts site_cart=self.tmp.sites_shifted[i_seq]) File "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/crystal/__init__.py", line 609, in correct_special_position raise AssertionError(error_message) AssertionError: Excessive special position correction: unit_cell: (56.278, 67.256, 106.26, 90, 90, 90) space_group_info: P 21 2 2 special_op: 1/2,y,1/2 site_frac: (0.5090941495765681, 0.42722892547242985, 0.5083083194012079) site_special_frac: (0.5, 0.42722892547242985, 0.5) distance_moved: 1.02047 Phenix v. 1.8.4-1496 -- 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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r-free output by resolution shell
by Ursula Schulze-Gahmen 10 Oct '13

10 Oct '13

Where can I find an output of Rfree in resolution shells? I ran phenix.model_vs_data and I don't see it there. I also didn't find it in the log-files of refinement. Maybe I am just overlooking it. Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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Project Database Location
by David Shin 10 Oct '13

10 Oct '13

Hi - I had a computer disk go down and want/need to migrate files over manually. I just reinstalled a 1.8.3 version of phenix from a disk image onto OS X 10.6.8. Upon launch, it appears it cannot find my old project database. I was wondering if this is something that can relatively easily migrated over from my backup disk, and where it lives. Thanks, Dave -- David Shin, Ph.D Lawrence Berkeley National Labs 1 Cyclotron Road MS 83-R0101 Berkeley, CA 94720 USA

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Worse R factor with newer version of phenix
by Jan van Agthoven 09 Oct '13

09 Oct '13

Hi everyone, I've been working on a low resolution structure (3.6A) which was previously refined with phenix 1.8_1069 (with a reference model, strategy=individual_sites,individual_adp ). I used the same input files and parameters and ended up with significantly different R factors. Start: r_work = 0.2850 r_free = 0.3189 bonds = 0.005 angles = 1.059 Final: r_work = 0.2609 r_free = 0.3160 bonds = 0.003 angles = 0.997 For the old version and Start: r_work = 0.2779 r_free = 0.3183 bonds = 0.006 angles = 1.141 Final: r_work = 0.2889 r_free = 0.3303 bonds = 0.021 angles = 2.737 with the new version 1.8.4 Remarkably it also came with an increased number of C-beta deviation (0 against 16!). Adding tls refinement or ramachandran restrains did not help. Now because I was using the .eff file of an old version of phenix, it came with a long list of unused parameters. These parameters however were all used by default. What should I do? Should I go back to this old phenix, or is there a way to improve the result? Thanks,

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