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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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Run time error while refining
by Subhani Bandara 22 Jun '12

22 Jun '12

Hi everyone, I got the following error message while running refinement in mac, using PHENIX-1.8-1069. This occured when refined after editing Ramachandran outliers in coot, without applying Ramachandran restraints. Not sure wether it has something to do with this. RuntimeError : Estimated memory allocation for cubicles exceeds max_number_of_bytes: This may be due to unreasonable parameters: cubicle_edge=5 space_span=(3528.41,3528.41,3442.53) n_cubicles=(706,706,689) max_number_of_bytes=2147483648 Any suggestions! Thanks Subhani

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error TLS groups
by Christian Roth 22 Jun '12

22 Jun '12

Dear Phenix developers, If I want use the automatic TLS definition the following error appears. At least the first error line with invalid iteral does also appear int the last verification step of the validation against the supplied sequence file. I have a PMS modified Serine could that cause the problem, because with other pdb's it works. Best Regards Christian RuntimeError : Error in subprocess! Original error: invalid literal for int() with base 10: '' Original traceback: File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/libtbx/thread_utils.py", line 233, in run return_value = self._target(self._args, self._kwargs, self._c) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/command_line/find_tls_groups.py", line 901, in __call__ xray_structure=self.xray_structure) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/command_line/find_tls_groups.py", line 729, in find_tls ssm.find_automatically(log=out) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/secondary_structure/__init__.py", line 334, in find_automatically self.sec_str_from_pdb_file = self.find_sec_str(log=log) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/secondary_structure/__init__.py", line 381, in find_sec_str allow_none=True) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/iotbx/pdb/secondary_structure.py", line 425, in process_records secondary_structure = annotation(records=records) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/iotbx/pdb/secondary_structure.py", line 62, in __init__ self.helices = parse_helix_records(records) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/iotbx/pdb/secondary_structure.py", line 217, in parse_helix_records helix_class=string.atoi(line[38:40]), File "/userdata-2/christian/phenix-1.8-1069/build/intel- linux-2.6/base/lib/python2.7/string.py", line 403, in atoi return _int(s, base) Traceback (most recent call last): File "/userdata-2/christian/phenix-1.8-1069/phenix/wxGUI2/Programs/Refine/TLS.py", line 140, in OnFindTLS self.find_tls_groups() File "/userdata-2/christian/phenix-1.8-1069/phenix/wxGUI2/Programs/Refine/TLS.py", line 103, in find_tls_groups callback=None) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/wxtbx/process_control.py", line 348, in run_function_as_process_in_dialog dlg.handle_error() File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/wxtbx/process_control.py", line 302, in handle_error %s""" % (str(exception), traceback)) RuntimeError: Error in subprocess! Original error: invalid literal for int() with base 10: '' Original traceback: File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/libtbx/thread_utils.py", line 233, in run return_value = self._target(self._args, self._kwargs, self._c) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/command_line/find_tls_groups.py", line 901, in __call__ xray_structure=self.xray_structure) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/command_line/find_tls_groups.py", line 729, in find_tls ssm.find_automatically(log=out) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/secondary_structure/__init__.py", line 334, in find_automatically self.sec_str_from_pdb_file = self.find_sec_str(log=log) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/secondary_structure/__init__.py", line 381, in find_sec_str allow_none=True) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/iotbx/pdb/secondary_structure.py", line 425, in process_records secondary_structure = annotation(records=records) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/iotbx/pdb/secondary_structure.py", line 62, in __init__ self.helices = parse_helix_records(records) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/iotbx/pdb/secondary_structure.py", line 217, in parse_helix_records helix_class=string.atoi(line[38:40]), File "/userdata-2/christian/phenix-1.8-1069/build/intel- linux-2.6/base/lib/python2.7/string.py", line 403, in atoi return _int(s, base) -- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319

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phenix.mr_model_preparation
by Alexander Batyuk 21 Jun '12

21 Jun '12

Dear all, I'm trying to run phenix.mr_model_preparation in phenix 1.8-1069 with a .hhr file but it fails with Reading homology search file: 4671015.hhr Sorry: Uninterpretable: 'Q ss_pred cccccchHHHHHHHHHHHHHHHHHhhhchheEEE etc. Could somebody point me to the right direction, please? Thank you and best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

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phenix.refine and torsion-angle ncs
by Antony Oliver 21 Jun '12

21 Jun '12

Dear phenix.bb How do I specifically exclude particular amino acids from torsion-angle ncs? >From the GUI, it is not obvious. In a couple of my chains, one or two amino acids are in definite crystal contacts, and are therefore in a different rotamer/conformation compared to the other ncs-related copies. Unfortunately, I can't seem to find the right option / keyword to stop the refinement job moving these side-chains to agree with the rotamers found in the other molecules of the asymmetric unit. Many thanks, Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oliver(a)sussex.ac.uk<mailto:[email protected]> tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512

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Re: [phenixbb] bad geometry problem
by Qian Sarah 20 Jun '12

20 Jun '12

> > > Hi Pavel Thank you so much! The information is VERY detailed and I learnt a lot! Thanks to phenixbb! > > 2012/6/21 Pavel Afonine <pafonine(a)lbl.gov> > >> Hi Sarah, >> >> thanks for sending me the data. I spent 15 minutes trying a few things >> and here is the statistics I get: >> >> r_work = 0.2454 r_free = 0.2700 >> MOLPROBITY STATISTICS. >> ALL-ATOM CLASHSCORE : 13.60 >> RAMACHANDRAN PLOT: >> OUTLIERS : 0.89 % >> ALLOWED : 5.33 % >> FAVORED : 93.78 % >> ROTAMER OUTLIERS : 8.64 % >> CBETA DEVIATIONS : 0 >> >> which isn't that bad compared to the starting point: >> >> r_work = 0.2469 r_free = 0.2613 >> MOLPROBITY STATISTICS. >> ALL-ATOM CLASHSCORE : 48.87 >> RAMACHANDRAN PLOT: >> OUTLIERS : 2.49 % >> ALLOWED : 5.33 % >> FAVORED : 92.18 % >> ROTAMER OUTLIERS : 29.47 % >> CBETA DEVIATIONS : 10 >> >> Here is what I did (it's just one of possible ways of doing this; other >> scenarios may works as good as this one or better!): >> >> - add H atoms: >> >> phenix.reduce model.pdb > model_H.pdb >> >> - then run a quick geometry regularization: >> >> phenix.pdbtools model_H.pdb --geom >> >> - then strip off H: >> >> phenix.reduce -trim model_H_regularized.pdb > start.pdb >> >> - then run refinement using NCS and Ramachandran plot restraints: >> >> phenix.refine start.pdb def_data.mtz main.ncs=true --overwrite >> output.prefix=def2 main.number_of_mac=5 ramachandran_restraints=true >> rama_potential=emsley strategy=individual_sites+**individual_adp >> >> - then take outcome of previous refinement and run the same refinement >> plus weights optimization: >> >> phenix.refine def2_001.pdb def_data.mtz main.ncs=true --overwrite >> output.prefix=def3 main.number_of_mac=5 ramachandran_restraints=true >> rama_potential=emsley strategy=individual_sites+**individual_adp >> optimize_xyz=true nproc=6 >> >> Also, looking at the original maps I see a lot of places where simple >> fixing in Coot is just obvious, for both - rotamers and Ramachandran >> outliers. So you should do it first of all. >> >> Also, use Ramachandran restraints ONLY to preserve good starting model >> and NOT to fix problems. >> >> All in all, geometry problems you were concerned about are all easily >> fixable. One of the reason why these problems arise is that the map is >> really looking like 3A resolution map, may be even worse; plus there are >> places in the model that you need to fix manually (refinement would not be >> able to fix them). >> >> I will send you the files off-list. >> >> >> Pavel >> >> On 6/19/12 1:17 AM, Qian Sarah wrote: >> >>> Hi, this may not be a new problem, but I tried every stretagy that I >>> know from bb, but the geometry is still very bad. So I wish I can get some >>> help from here. >>> Crystal information: >>> SAD data. Resolution 3.0. There is no anisotropy in the data. >>> R/Rfree : 22.7/26.8 (Rfree-flag is always from the Refine_data.mtz file >>> generated after the first refinement.) >>> RMS(bonds):0.02 >>> RMS(angles): 1.453 >>> Ramachandran outliers: 3.0% >>> Ramachandran favored: 91.2% >>> Rotamer outliers: 18.7% !! >>> Clashscore: 31.84 >>> overall score: 3.47 >>> I tried different strategies, like autobuild and then refine; set >>> wxu/wxc=0.3/0.3; turn on "Ramachandran restrains", "fix bad sidechain >>> romaters"etc, however the paramters are still very bad, especially the >>> rotamer outliers. Then I rebuild them manually in coot,after refinement the >>> parameters are even worse. >>> p.s. phenix version: phenix-1.7.3-dev-1046. >>> Thank you very much! >>> best, >>> Sarah >>> >> >> >

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fixing weights
by Morten Groftehauge 20 Jun '12

20 Jun '12

Hi all, I tried specifying wxc, wxu, wxu_scale and wxc_scale as you can see from the log file: target_weights { wxc_scale = 0.50001 wxu_scale = 0.49999 fix_wxc = 6 fix_wxu = 0.35 } but the refinement proceeds with the default values for _scale: ========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 6.000000 wxc_scale = 1.000 wc = 1.000 | | angle between x-ray and geometry gradient vectors: None (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.350000 wxu_scale = 0.500 wu = 1.000 | | angle between Xray and ADP gradient vectors: None (deg) | |-----------------------------------------------------------------------------| I am running dev-1082, used the GUI for phenix.refine. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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R-factor calculation
by Abhinav Kumar 20 Jun '12

20 Jun '12

Hi, Is it possible to specify a different high resolution cutoff (than what's in data file) in phenix.model_vs_data for R-factors calculation? -- Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992

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bad geometry problem
by Qian Sarah 20 Jun '12

20 Jun '12

Hi, this may not be a new problem, but I tried every stretagy that I know from bb, but the geometry is still very bad. So I wish I can get some help from here. Crystal information: SAD data. Resolution 3.0. There is no anisotropy in the data. R/Rfree : 22.7/26.8 (Rfree-flag is always from the Refine_data.mtz file generated after the first refinement.) RMS(bonds):0.02 RMS(angles): 1.453 Ramachandran outliers: 3.0% Ramachandran favored: 91.2% Rotamer outliers: 18.7% !! Clashscore: 31.84 overall score: 3.47 I tried different strategies, like autobuild and then refine; set wxu/wxc=0.3/0.3; turn on "Ramachandran restrains", "fix bad sidechain romaters"etc, however the paramters are still very bad, especially the rotamer outliers. Then I rebuild them manually in coot,after refinement the parameters are even worse. p.s. phenix version: phenix-1.7.3-dev-1046. Thank you very much! best, Sarah

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Source code build - overriding compiler choice
by Graeme Winter 18 Jun '12

18 Jun '12

Hi Folks, On my macbook with lion and a source code build, I always set --compiler=gcc for cctbx and this works fine. Just tried a source code build of phenix which failed because it picked up clang, so how do I override this in the install script? I didn't see the option from the install script: Graemes-MacBook-Pro:phenix-installer-dev-1078 graeme$ ./install --help Usage: install [options] Options: --prefix=<path> Determines PHENIX installation path, which will be <path > /phenix-[version] --overwrite Forces overwriting of installed packages --nproc=number Number of processors to use in compilation --base-only Do not compile PHENIX sources (cctbx, phaser, resolve, etc.) --no-gui Do not compile and install GUI components --no-apps Don't create Mac app launcher icons --app-prefix=<path> Path for Mac app launchers (default: /Applications) --noopt Turn off optimization during compilation --debug Turn on debugging during compilation --openmp Try to use OpenMP if supported by compiler --force-compile Force compilation of source --binary Force a binary install if binaries and source are both available --source Force a source install if binaries and source are both available --no-packages Do not install other packages such as PHASER --alias-mtype=<string> Force installation from a different machine type e.g. --alias-mtype=intel-linux-2.4 [for binary installations only] --try-unsupported Try source installation on an unsupported platform --help Print this help message Thanks, Graeme

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