- phenixbb - phenix-online.org

segmented rigid body refinement
by Gino Cingolani 12 Jul '12

12 Jul '12

Hi all, I'm refining a large oligomeric structure at low res (~6A). I'd like to define groups to use for 'segmented rigid body refinement'. Is there any rational way to define 'segments'? My macromolecule is already an oligomer on its own, so, intuitively, each protomer is a segment. Thanks, Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) ________________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Nathaniel Echols [nechols(a)lbl.gov] Sent: Thursday, July 12, 2012 7:44 AM To: PHENIX user mailing list Subject: Re: [phenixbb] RFZ is higher than TFZ On Thu, Jul 12, 2012 at 12:38 AM, 周文昌 <wenchangyu2006(a)gmail.com> wrote: > I had one problem using phaser-MR to solve my structure. Phaser-MR gives me > one solution with TFZ=15.4 and LLG=165 which seems to be promising but > phenix.refine does not give me a low R values (0.4884/0.5424). I went back > and checked the solution from phaser-MR, I found RFZ=18.8, higher than TFZ. > Does anyone think this is a problem to solve my structure? > > The space group is C121, I believe there are 4 copies of my search model in > ASU. What is the resolution, and what is the sequence identity of the search model? I don't know whether the high RFZ means anything, but the first thing I would check is whether the packing of the MR solution makes sense; Phaser will do a good job preventing molecules from overlapping (unless you changed it to use much less conservative criteria), but it won't guarantee that the molecules pack into a nice continuous lattice. If there are big gaps, it may not be a real solution. I think we need to add an entire FAQ page for high R-factors. However, there are an increasing number of tools and/or tricks in Phenix to deal with problems like this - in approximate order of runtime: - run phenix.refine for more cycles - at least 20. See this paper for an example of why this can be important: http://journals.iucr.org/d/issues/2012/07/00/kw5044/index.html - use phenix.morph_model (refer to previously mentioned paper) - use phenix.den_refine (or DEN in CNS) - use MR-Rosetta Also, if you're willing to share your data with us, we're collecting difficult-to-refine structures for benchmarking new methods. (It will of course be kept confidential.) -Nat _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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v1.8 bug ? memory allocation crash in map calculation (phenix.refine, phenix.maps)
by Phil Jeffrey 12 Jul '12

12 Jul '12

This is in F432 in a=b=c=340A at 2.85A resolution. Mac OSX 10.5.8, the machine has 8Gb memory of which something like 6Gb is hanging around begging to be used. 1,327,104,000 if that's in bytes doesn't seem all that excessive. On the other hand, 340*340*340= 39,419,600 so it's perhaps a little greedy. Limits set by shell: phil% limit cputime unlimited filesize unlimited datasize unlimited stacksize 65532 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 266 phenix.refine does the same thing right at the end, which is kind of a shame since it takes quite a long time to run. phenix.maps does the same thing even if I ask it just to generate F,phase in MTZ format. [snip] Compute maps. Python(632) malloc: *** mmap(size=1327104000) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug show_stack(1): /usr/local/phenix-1.8-1069/cctbx_project/cctbx/miller/__init__.py(3067) double_step_filtration show_stack(2): /usr/local/phenix-1.8-1069/cctbx_project/mmtbx/maps/__init__.py(416) map_coefficients_from_fmodel show_stack(3): /usr/local/phenix-1.8-1069/cctbx_project/mmtbx/maps/__init__.py(543) __init__ show_stack(4): /usr/local/phenix-1.8-1069/build/mac-intel-osx/../../cctbx_project/mmtbx/command_line/maps.py(325) run show_stack(5): /usr/local/phenix-1.8-1069/build/mac-intel-osx/../../cctbx_project/mmtbx/command_line/maps.py(402) <module> Bus error (Python call stack above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical.

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RFZ is higher than TFZ
by 周文昌 12 Jul '12

12 Jul '12

Dear all, I had one problem using phaser-MR to solve my structure. Phaser-MR gives me one solution with TFZ=15.4 and LLG=165 which seems to be promising but phenix.refine does not give me a low R values (0.4884/0.5424). I went back and checked the solution from phaser-MR, I found RFZ=18.8, higher than TFZ. Does anyone think this is a problem to solve my structure? The space group is C121, I believe there are 4 copies of my search model in ASU. thanks, Wenchang

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sigma_iobs_rejection_criterion
by Yarrow Madrona 10 Jul '12

10 Jul '12

Hello, I am refining a structure using a.eff file that I generated in Phenix version 1.7 GUI and later ran in the command line. When I try to run the same refinement in Phenix V.1.8 I get the following error: For French and Wilson scaling, sigma_iobs_rejection_criterion must be set between -4.0 and -1.0 I see that it was set to zero previously. My questions are: 1. Is this the same observed criterion that is reported in the RCSB Deposition? 2. To be honest I don't understand what this is. Is it a limit for the error in Iobs, below which the reflection will be discarded? 3. What is a reasonable setting for this input and how does it change the refinement? Thank you (I appreciate your help as I know these may be very basic questions). -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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Phenix autosol error 2L MAD
by Graeme Winter 10 Jul '12

10 Jul '12

Hi Folks, 2L MAD data set where SHELXC/D/E works fine I (repeatedly) get this error, through GUI or scripts... resolution: 1.7 recommended_resolution: 1.9 datafile_for_hyss: /Users/graeme/projects/test/12287_build/AutoSol_run_10_/TEMP0/ANISO_subset_PHX_I(+)_WAVE1.sca_ano_1.sca aniso_corrected: True aniso_b_min: 13.2 aniso_range_of_b: 6.8 RUNNING HYSS on ANISO_subset_PHX_I(+)_WAVE1.sca_ano_1.sca from PDS as miller arrays *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoSol_hyss: HYSS failed...Probably no iso or ano differences... ******************************************************************************** *************ERROR ENDING ******************* The data set works fine with a third (radiation damaged) data set. There is also a massive anomalous signal in the data (2L) as it stands. here's the PHIL: autosol { seq_file = 12287.seq sites = 8 atom_type = Se crystal_info { unit_cell = 51.59 51.59 157.69 90 90 90 space_group = "P 43 21 2" solvent_fraction = 0.52 chain_type = PROTEIN resolution = 0 change_sg = True } wavelength { data = subset.mtz lambda = 0.97966 f_prime = -9.9 f_double_prime = 3.9 labels = 'I(+)_WAVE1 SIGI(+)_WAVE1 I(-)_WAVE1 SIGI(-)_WAVE1' } wavelength { data = subset.mtz lambda = 1.00000 f_prime = -3.3 f_double_prime = 0.5 labels = 'I(+)_WAVE2 SIGI(+)_WAVE2 I(-)_WAVE2 SIGI(-)_WAVE2' } } Have I done something wrong? Thanks, Graeme

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special position
by Karolina Michalska 09 Jul '12

09 Jul '12

Hi all, I'm refining a structure with a phosphate ion on a 3-fold axis. I set occupancy manually to 0.33 and after refinement the ion has huge B-factor (close to 100) and there is a lot of positive electron density. I found somewhere that phenix recognizes special positions and there is not need to adjust occupancy manually. so I set it to 1 again and re-refined. This time my phosphate sits in a mixture of negative and positive density with B factor around 90 (for comparison Refmac refines it to ~20). Now I'm confused which procedure to follow. Karolina

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I/O error in writing very large B-factors
by Phil Jeffrey 09 Jul '12

09 Jul '12

This occurs at the end of refinement. Quite why it's trying to *read* from a string with Fortran-esque overflow formatting while in a writing step I don't know, but the PDB file gets truncated at REMARK IF THIS FILE IS FOR PDB DEPOSITION: REMOVE ALL FROM THIS LINE UP. The structure is not idyllic, clearly, but I'd like to see the extent of the problem rather than just the first atom. Got to be pretty easy to trap for and map to 999.99 either on the way in or out. Writing refined structure to PDB file: /Users/phil/Structures/reference_models/start_refine_001.pdb n_use = 21264 n_use_u_iso = 21264 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 21264 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 21264 Traceback (most recent call last): File "/usr/local/phenix-1.7.3-928/build/mac-intel-osx/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.7.3-928/phenix/phenix/refinement/command_line.py", line 105, in run refine_object.write_refined_pdb(f_pdb) File "/usr/local/phenix-1.7.3-928/phenix/phenix/refinement/driver.py", line 1379, in write_refined_pdb ignore_hd = not self.neutron_refinement) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model_statistics.py", line 589, in __init__ ignore_hd = ignore_hd) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model_statistics.py", line 504, in __init__ molprobity_scores=True) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model.py", line 1063, in geometry_statistics molprobity_scores = molprobity_scores) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model_statistics.py", line 112, in __init__ self.clashscore_obj.analyze_clashes(hierarchy = pdb_hierarchy) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/validation/clashscore.py", line 182, in analyze_clashes self.pdb_hierarchy = pdb.hierarchy.input(pdb_string=input_str).hierarchy File "/usr/local/phenix-1.7.3-928/cctbx_project/iotbx/pdb/hierarchy.py", line 1044, in __init__ source_info=source_info, lines=flex.split_lines(pdb_string)) File "/usr/local/phenix-1.7.3-928/cctbx_project/iotbx/pdb/__init__.py", line 582, in input return ext.input(source_info=source_info, lines=lines) ValueError: string, line 5148: ATOM 17 N ILE A 268 -16.878 -22.262 49.415 1.00****** A N ------------------------------------------------------------^ not a floating-point number. Phil Jeffrey Princeton

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Iridium hexamine problems with eLBOW
by Benoît Masquida 07 Jul '12

07 Jul '12

I experience problems generating a correct CIF file for iridium hexamine (IRI in the eLBOW database). The geometry is supposed to be octahedral and eLBOW outputs a prism regardless of the options checked in the GUI. eLBOW actually does the same for the octahedral Mg(OH2)6. Does someone know how to rule this out? Thanks to everybody. Ben -- Benoît Masquida Chargé de Recherche CNRS IBMC Strasbourg UPR 9002 ARN b.masquida(a)ibmc-cnrs.unistra.fr +33 (0)3 88 41 70 45 +33 (0)6 70 23 79 50 +33(0)3 88 60 22 18 (fax)

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Subject: no kidding - we need small crystals!
by jens j birktoft 05 Jul '12

05 Jul '12

Hi everybody, Any suggestions regarding how to generate small!! crystals? Yes, in this case that is what we want While we can generate crystals of size 100-500 microns, this time we something in the range of .5-5 microns. Any ideas and suggestions would be greatly appreciated, Cheers Jens

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ask refinement question including an aligo as the ligand
by crystallogrphy 05 Jul '12

05 Jul '12

Hi, I want to refine my structure including a sugar oligomer as the ligand in Phenix GUI. I first put each subunit into the density and merge them together as the oligomer in Coot. Then I merged the oligomer coordinates to the protein file. Then I run phenix.elbow to get the cif file. Finally, I run phenix.refine. However, the oligomer units were pushed away from each other. I guess I need to modify the cif file to link the oligo units together. Does anyone know how I can I do it? thanks!

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Re: [phenixbb] phenixbb Digest, Vol 80, Issue 1
by Matthew J. Whitley 04 Jul '12

04 Jul '12

Hello, One simple thing that might be the problem: As I'm sure you know, oligosaccharides are formed via intermolecular dehydration reactions. If I understand you correctly, you built the oligosaccharide by loading the component monomers into the density in Coot and then joined them together. Whenever two sugars are joined together, three atoms are given off as a water molecule. Did you actually delete the appropriate oxygen and two hydrogens from your coordinates for each glycosidic linkage in your structure? If you didn't, then it doesn't matter whether you told Coot or Phenix that the monomers or linked, you'll still have atoms trying to occupy the same space and thus the refinement will blow them apart. Not that I have EVER made that mistake myself . . . Similar topics have come up on the Phenix BB before. For other possibly useful information, see: http://phenix-online.org/pipermail/phenixbb/2012-April/018390.html http://www.phenix-online.org/pipermail/phenixbb/2009-October/013951.html Good luck! Matthew --- Matthew J. Whitley, Ph.D. Postdoctoral Research Fellow Angela Gronenborn Lab Department of Structural Biology University of Pittsburgh School of Medicine On Wed, July 4, 2012 7:55 pm, phenixbb-request(a)phenix-online.org wrote: > > > Message: 14 > Date: Wed, 4 Jul 2012 15:28:09 -0400 > From: crystallogrphy <qunwan1(a)gmail.com> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: [phenixbb] ask refinement question including an aligo as the > ligand > Message-ID: > <CANcEHNi95ss+Tst8+8JVTK3=B598HjC_NNg5N7_=6-whdMTXpQ(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I want to refine my structure including a sugar oligomer as the ligand in > Phenix GUI. > > I first put each subunit into the density and merge them together as the > oligomer in Coot. Then I merged the oligomer coordinates to the protein > file. Then I run phenix.elbow to get the cif file. Finally, I run > phenix.refine. However, the oligomer units were pushed away from each > other. I guess I need to modify the cif file to link the oligo units > together. Does anyone know how I can I do it? > > thanks!

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need subscription
by Afshan Begum 03 Jul '12

03 Jul '12

Dear Sir I have subscribe successfully to the phenixbb but i have not receive or involved in the discussion board could you kindly help ? Best Regards AFSHAN

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Question about mr-sad
by Edward A. Berry 02 Jul '12

02 Jul '12

in doing SAD phasing with the option: input_partpdb_file=MR.pdb Is it assumed MR.pdb is already located in the cell, or is it a model to be used in MR assisted by information from the heavy atom sites? Thanks, eab

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Re: [phenixbb] Default anisotropic B-factor refinement in phenix.refine?
by Filip YABUKARSKI 02 Jul '12

02 Jul '12

Hello again, First thank you very much for the response But in this case after the second run of phenix.refine i will lose the TLS contribution and the anisoU lines (?). How am I supposed to continue with TLS then (given it lowers my R factors i would be happy to keep it) and be sure that i do not refine anisotropic ADPs? Or you mean that i can do the 2 consecutive runs (with and without TLS) in the end of the refinement? Sorry if I got something wrong Filip On 2012-07-02 18:58, Pavel Afonine wrote: > Hi Filip, > > phenix.refine manual may need an update.. > > At 3A resolution if you run two consecutive refinements first with > TLS and the next one without TLS then in the second run anisotropic > ADPs will be converted to isotropic automatically. This is done by > phenix.refine to prevent accidental refinement of individual > anisotropic ADPs in such cases. The keyword and threshold are: > switch_to_isotropic_high_res_limit=1.5. > > Pavel > > On 7/2/12 9:47 AM, Filip YABUKARSKI wrote: >> Hello, >> >> I recently started to refine a structure with phenix.refine for a >> first time. It is a 3A dataset with NCS of 8. For the refinement i >> wanted to use TLS groups as well as individual B-factors >> (data/parameter ratio should be fine with ncs of 8) and after several >> cycles of refinement i get the Rfac of 20 and Rfree of 24 which is >> quite good (i also use simulated annealing, Secondary structure >> restraints and NCS restraints). Re-reading the refinement manual I >> realized that by using a PDB file which comes from a phenix.refine >> with TLS in the next refinement i am probably doing an anisotropic >> B-factor refinement for each atom, which in my case is not justified. >> I found a post on ccp4bb from 19 Fev 2009 discussing this issue but >> for me it is still not very clear. By reading the PDB i got from >> phenix.refine (version 1.7.3) it is not very clear (at least for me) >> if the refinement was with TLS groups and individual isotropic >> B-factors or with anisotropic B-factors. Basically my question is: if >> the input PDB has already anisoU records from a previous phenix.refine >> with TLS groups is the new phenix.refine going to use isotropic >> individual B-factors or anisotropic ones? (Even if in my case one can >> assume that i can probably use anisotropic B-factor refinement (24000 >> unique reflections with ncs of 8 vs. 6000 atoms in total) this is >> rarely the case for non-atomic resolution datasets) I would be very >> happy if someone gives an explanation. Many thanks >> >> Cheers >> Filip

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Default anisotropic B-factor refinement in phenix.refine?
by Filip YABUKARSKI 02 Jul '12

02 Jul '12

Hello, I recently started to refine a structure with phenix.refine for a first time. It is a 3A dataset with NCS of 8. For the refinement i wanted to use TLS groups as well as individual B-factors (data/parameter ratio should be fine with ncs of 8) and after several cycles of refinement i get the Rfac of 20 and Rfree of 24 which is quite good (i also use simulated annealing, Secondary structure restraints and NCS restraints). Re-reading the refinement manual I realized that by using a PDB file which comes from a phenix.refine with TLS in the next refinement i am probably doing an anisotropic B-factor refinement for each atom, which in my case is not justified. I found a post on ccp4bb from 19 Fev 2009 discussing this issue but for me it is still not very clear. By reading the PDB i got from phenix.refine (version 1.7.3) it is not very clear (at least for me) if the refinement was with TLS groups and individual isotropic B-factors or with anisotropic B-factors. Basically my question is: if the input PDB has already anisoU records from a previous phenix.refine with TLS groups is the new phenix.refine going to use isotropic individual B-factors or anisotropic ones? (Even if in my case one can assume that i can probably use anisotropic B-factor refinement (24000 unique reflections with ncs of 8 vs. 6000 atoms in total) this is rarely the case for non-atomic resolution datasets) I would be very happy if someone gives an explanation. Many thanks Cheers Filip

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Postdoctoral Fellow & Scientific Officer / Higher Scientific Officer Positions at ICR, London, UK
by Sebastian Guettler 29 Jun '12

29 Jun '12

Dear PHENIX Community, We are currently looking for two motivated researchers to join our new, exciting research programme on the regulation and functions of ADP-ribosyltransferases: one Scientific Officer / Higher Scientific Officer and one Postdoctoral Fellow. Please see the job descriptions for the two positions and instructions on how to apply below. Best wishes, Sebastian Postdoctoral Fellow & Scientific Officer / Higher Scientific Officer Positions at ICR, London, UK In the Divisions of Structural and Cancer Biology of the Institute of Cancer Research (ICR; http://www.icr.ac.uk), our new team led by Dr. Sebastian Guettler has a vacancy for a Scientific Officer or early-career Higher Scientific Officer and a Post-doctoral Training Fellow. 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, where the laboratory will be physically based, has managed facilities for protein crystallography (crystallisation robots, x-ray diffractions systems), cryo-electron microscopy and protein production with expertise in multi-subunit expression systems (bacterial, yeast and insect cell expression, including a 60-litre fermentor). The Division is also well equipped with instrumentation for biophysical analysis (e.g., ITC, fluorescence-based methods, 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. Position 1: Post-doctoral Training Fellow (job reference number 1257974) Closing date of vacancy: 6 July 2012 Starting date of position: mid-October / early November 2012 Division: Structural Biology & Cancer Biology Team: Guettler Group Type of contract: fixed term Length of contract: 3 years in the first instance Salary range: £27,536 to £33,852 p.a. inclusive (depending on previous post-doctoral experience) Work location: London (Chester Beatty Laboratories, Chelsea) 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 and a sound knowledge of protein purification for structural analyses. Experience with recombinant DNA techniques, protein expression and purification as well as protein crystallography is essential. Experience in mammalian cell culture, enzymology or protein production in insect cells (MultiBac) would be of advantage. 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 1257974 for this position. 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. Position 2: Scientific Officer / Higher Scientific Officer (job reference number 1260528) Closing date of vacancy: 20 July 2012 Starting date of position: mid-October / early November 2012 Division: Structural Biology & Cancer Biology Team: Guettler Group Type of contract: fixed term Length of contract: 3 years in the first instance Salary range: £23,000 to £29,545 p.a. inclusive (depending on skills and experience) Work location: London (Chester Beatty Laboratories, Chelsea) The objective of this post will be to provide support within Dr. Guettler's laboratory for research into the structure and function of proteins. The post holder will work as a member of a multidisciplinary team investigating the functions and regulation of ADP-ribosyltransferases. The work will involve the production and purification of proteins and protein complexes, their characterisation, crystallisation and functional analysis. Applicants should minimally possess a BSc (or equivalent) in molecular biology, biochemistry or cell biology. Experience in molecular cloning, recombinant protein expression in E. coli and large-scale, crystallisation-grade protein purification is essential. Experience with protein production in insect cells (MultiBac) and mammalian cell culture would be of advantage. 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 1260528 for this position. 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. 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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k_sol and b_sol
by Luca Pellegrini 28 Jun '12

28 Jun '12

Hello, Where do I find the minimised values of k_sol and b_sol in phenix.refine? For some reason, they are not included in REMARK 3 of the pdb file after refinement, and I can't find them in the log file. Thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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Incorrect solvent modelling in Phenix.refine?
by David Briggs 27 Jun '12

27 Jun '12

Hi all, I'm refining a couple of structures of the same protein (well, point mutants) and I am consistently seeing large (6sig) negative difference map peaks within some cavities within my protein, present in both the datasets. As far as I understand, this is because the bulk solvent scaling parameters are either incorrect, or being incorrectly applied. I have tried a few things like applying the "Refine solvent mask (slow)" options, all to no avail. Resolution is 2.2Å and 2.5Å. Experimental phasing, Xtriage reports no abnormalities in the data. Is there anything that I am missing? Do I need to worry about this? Regards, Dave ============================ David C. Briggs PhD Father, Structural Biologist and Sceptic ============================ University of Manchester E-mail: david.c.briggs(a)manchester.ac.uk ============================ Webs : http://flavors.me/xtaldave Twitter: @xtaldave Skype: DocDCB ============================

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Error in phenix.autobuild
by Tanner, John J. 27 Jun '12

27 Jun '12

Can anyone shed light on the error below? The situation is that I have a ~90% complete model from refinement (r_work = 0.2415, r_free = 0.3167), and I want phenix.autobuild to build the rest of the structure. I issued this command: phenix.autobuild data=../ccp4/DrPRODH3-6_1_scala2.6Ang.mtz model=Refine_9/DrPRODH_refine_9.pdb seq_file=../seq/DrPRODH-noMet1.fasta rebuild_in_place=False nproc=3 I got this error: [tannerjj@europa AutoBuild_run_2_]$ tail -n20 AutoBuild_run_2_1.log Output space group: P 1 21 1 (No. 4) Columns of data in AutoBuild_run_2_/refinement_PHX.mtz: H K L FreeR_flag F_DrPRODH3-6 SIGF_DrPRODH3-6 Unit cell: (46.806, 95.875, 70.504, 90, 107.733, 90) Space group: P 1 21 1 (No. 4) Using AutoBuild_run_2_/refinement_PHX.mtz for refinement Correcting data file /titan/tanner/DrPRODH/ccp4/DrPRODH3-6_1_scala2.6Ang.mtz for anisotropy and writing to AutoBuild_run_2_/aniso_data_PHX.mtz Getting overall aniso B from datafile... *************ERROR ENDING ******************* **************************************** AutoBuild Input failed iotbx InternalError: /net/longnose/scratch2/phenix/phenix-1.7.3-928/cctbx_project/iotbx/mtz/dataset.cpp(97): IOTBX_ASSERT(strlen(label) < sizeof(column_ptr->label)) failure. **************************************** *************ERROR ENDING *******************

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occupancy group definition
by Christian Roth 26 Jun '12

26 Jun '12

Dear All, I have tried an occupancy refinement for a partially modifed residue. I have split the residue in altloc A and B and the modification (PMSF) is attached on B. I included the PMS moiety as part of the residue and gave them altloc B. I created the cif link. The refinement resulted in a strange mixture of occupancys for PMS around 0.8 and both Serins 0.23 an 0.77. So PMS is not part of the residue. I am not sure about the correct syntax for the constrained group. At the moment I have used constrained_group { selection = chain A and resseq 130 and altloc A selection = chain A and resname PMS and altloc B } However the Serine pat of altloc B refines to a value not compatible to the PMS values or the Altloc A value of the serine. How do I incorporate the altloc B for the serine? Thanks in advance for your help Christian

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geometry weight help
by 周文昌 25 Jun '12

25 Jun '12

Dear all, Last week, I played a little bit with geometry weight in phenix refinement. When I check the log file, what I found is that if I use wxc_scale and fix_wxc in my refinement, actually phenix will ignore the wxc_scale, while if I only use wxc_scale, phenix will follow the value specified in the command line, but the wxc value will change from one macro cycle to another cycle. Below shows one of my examples in which the wxc_scale values are ignored when I use wxc_scale and fix_wxc at the same time. Anyone has similar problems? Thanks for all your considerations. ################## Command line arguments: "../new-unique.mtz" "../3tx8.pdb" "fix_rotamers=true" "strategy=individual_adp+individual_sites" "wxc_scale=0.01" "refinement.input.xray_data.labels=FP,SIGFP" "fix_wxc=10" "--overwrite" refinement.target_weights.wxc_scale = 0.01 refinement.target_weights.fix_wxc = 10 wxc_scale = 0.01 fix_wxc = 10 | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 10.000000 wxc_scale = 1.000 wc = 1.000 | ... ################## Wenchang

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Diffractive Imaging Postdoctoral Scientist Opportunity
by Nicholas Sauter 25 Jun '12

25 Jun '12

I'd like to alert subscribers to an exciting postdoctoral scientist opportunity, using diffractive imaging to examine organelle-scale biological structures at the Linac Coherent Light Source. The job posting is listed at: http://academicemployment.chance.berkeley.edu/DetailsJobSearch.cfm?recordID… The advertised position is strongly oriented toward the development of computational methods. The successful candidate will join the group of Cheryl Kerfeld at UC Berkeley, and collaborate daily with scientists at LBNL. Informal inquiries may be directed to Nick Sauter, nksauter at lbl.gov Peter Zwart, phzwart at lbl.gov -- Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Physical Biosciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 64R0121 Berkeley, CA 94720-8118 (510) 486-5713

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dihedral restraints problem with alternate conformations
by Benoît Masquida 25 Jun '12

25 Jun '12

I am having an issue refining 2 superimposed MES molecules A and B (morpholino ethane sulfonic acid, buffer seen in the density). phenix.refine works fine up to the end where it crashes because of the following error: Duplicate dihedral restraints: tor id: var_10 residue: MES, conformer "A" atoms: "HETATM 3993 O1 AMES T 1 .*. O " "HETATM 3994 C2 AMES T 1 .*. C " "HETATM 3995 C3 AMES T 1 .*. C " "HETATM 3996 N4 AMES T 1 .*. N+1" I can't see where is the conflict since all atoms have distinct labels and I provided the CIF file generated with phenix.elbow. What should I change to circumvent this problem? Thanks Ben

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mr_rosetta problem
by Andreas Forster 24 Jun '12

24 Jun '12

Dear all, especially Tom T and Laurie Betts: I've recently installed phenix-dev-1084 and Rosetta 3.4 on RHEL 6.2. No problem. When I test the rosetta commands with phenix_regression.wizards.test_command_line_rosetta_quick, the first 12 of 39 tests succeed but test_prerefine fails and the process aborts. This is the error in the log file: /csb/soft/Linux64/share/rosetta3.4/rosetta_source/bin/mr_protocols.default.linuxgccrelease: error while loading shared libraries: libdevel.so: cannot open shared object file: No such file or directory libdevel.so exists, in the right place I venture to say: ls -l /csb/soft/Linux64/share/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.4/libdevel.so -rwxr-xr-x. 1 csbadmin csb 6437 Jun 23 18:44 /csb/soft/Linux64/share/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.4/libdevel.so Besides the tests failing, the actual mr_rosetta run fails as well, as one would expect, with the same "missing library" error. This problem has been reported before (http://www.phenix-online.org/pipermail/phenixbb/2011-May/017157.html), but I can't find a solution. Is there one? Thanks. Andreas

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Phenix version 1.8 released
by Paul Adams 22 Jun '12

22 Jun '12

The Phenix developers are pleased to announce that version 1.8 of Phenix is now available. Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical interface: ==================== - New GUIs: phenix.multi_crystal_average, phenix.morph_model, phenix.table_one, phenix.find_peaks_holes - Improved layout for AutoBuild and reflection file editor GUIs - Editor for custom bond/angle/plane restraints in phenix.refine - Project groups: manage defaults for similar projects General: ======== - New very fast bulk-solvent and overall anisotropic scaling procedure - Experimental Windows installer (32-bit only) - Improved support for anomalous difference arrays (F SIGF DANO SIGDANO ISYM) - New commands: phenix.den_refine, phenix.find_peaks_holes - Overall Molprobity score now calculated in phenix.model_vs_data and the validation/refinement GUIs Refinement: =========== - Change in default NCS restraints behavior: - use torsion-angle parameterization - restraints on NCS-related B-factors turned off - Automatic matching of chains to reference model; allows multiple chains to be restrained to a single reference chain - Support for multiple reference model files - New method for filling of missing Fobs using simple density modification Molecular Replacement: ====================== - phaser (version 2.5): - TNCS support enabled by default for both MR and SAD Experimental Phasing and Model Building: ======================================== - AutoSol: - TNCS support for SAD phasing Miscellaneous: ============== - phenix.pdbtools: - ability to set atomic charge field (used for X-ray scattering factors and VDW radii in nonbonded restraints) - phenix.find_peaks_holes (new command): - standalone map peak search program: highlight difference map features - includes analysis of anomalous maps, flag suspicious "water" molecules - phenix.maps: - simplified execution on command line: "phenix.maps model.pdb data.mtz" - generates default map coefficients (2mFo-DFc, mFo-DFc, anomalous if available) and 2mFo-DFc CCP4-format map. - phenix.fetch_pdb: - added --maps option: generates 2mFo-DFc and mFo-DFc map coefficients - phenix.get_cc_mtz_pdb: - added atom_selection keyword: compute CC for a subset of atoms - phenix.real_space_correlation: - simplified execution on command line: "phenix.real_space_correlation model.pdb data.mtz" - calculates CC of model to 2mFo-DFc map - added atom_selection keyword: compute CC for a single selection (instead of per-atom or per-residue statistics) For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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