- phenixbb - phenix-online.org

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 03 Jul '12

03 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 03 Jul '12

03 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 03 Jul '12

03 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 30 Jun '12

30 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 28 Jun '12

28 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. 28 Jun '12

28 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 27 Jun '12

27 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 26 Jun '12

26 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 26 Jun '12

26 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 26 Jun '12

26 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 25 Jun '12

25 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 23 Jun '12

23 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 23 Jun '12

23 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 22 Jun '12

22 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 21 Jun '12

21 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 >>> >> >> >

1 0

fixing weights
by Morten Groftehauge 21 Jun '12

21 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

3 3

R-factor calculation
by Abhinav Kumar 21 Jun '12

21 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

2 4

bad geometry problem
by Qian Sarah 21 Jun '12

21 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

3 3

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

2 3

MR_Rosetta
by Heather Condurso 16 Jun '12

16 Jun '12

Hello all, I am working on a structure for which a good molecular replacement model doesn't really exist ( highest sequence similarity is 24% for a protein with completely different function and even worse for proteins with a more similar function). As I try and solve the phase with Se-Met derived protein, I thought I would try and use MR_rosetta and see what happens. I have also tried to use pyrosetta to generate better models, but the structure alignments suggest my protein to be primarily composed of beta sheets so the models from ab initio methods aren't great. I am using the GUI and have given my sca file, a sequence file, the 3 and 9 fragment files, and both the global and local alignment hhr files. I thought that phenix would use the hhr alignments to pull models directly from the pdb, but without giving a model pdb, MR_rosetta fails. So my question is how do I input the models? Should I download each of the pdbs and clean them up a bit? How many should I include? I unde! rstand the more I include the more computing time this will take. Can you give any recommendations as to other parameters to change keep the computing time down initially to identify the best model before extensive time is used? I appreciate any help you may be able to provide, Heather Condurso UF-Department of Chemistry condurso(a)ufl.edu

3 6

alternate conformation clashes
by Timothy Springer 15 Jun '12

15 Jun '12

We have a 1.4 Å structure with two pseudo-symmetry related A and B chains that form a super b-sheet. An 8-residue loop has two quite different alternate, backbone conformations. When we refine the occupancy of these loops, they come out to 0.51 and 0.49, consistent with them being mutually incompatible (i.e., forced to be 0.50 and 0.50 in the ideal situation). Indeed, clashes would exist between the A chain A alternate and the B chain A alternate, but when these are A and B alternates, there is no clash. Since these are in separate chains, Phenix has no problem with an A and A clash. There is a second loop, non-contiguous in sequence, that also has clashes with one of these. We refine each of the two clashing loops as the A conformat ion. Since these are separate loops, Phenix does not seem to care and seems to treat the A conformation of one loop as if it is compatible with the B conformation of the other loop. This is great that Phenix is so forgiving, but my concern is that shouldn't by convention we reassign the conformations so that the A conformations are all compatible within the same monomer? Is there some formal convention on this, and will PDB ask us to reassign these? In a closely related 1.7 Å lattice, we have a single molecule per asymmetric unit, and now the relationship is between two symmetry-related molecules. The two conformations of loops are similar as in the 1.4 Å structure. Here, we have to keep the same alternate conformation name, and thus have a clash between A and A loops 1 but not A and B loops 1. Again there is a clash between A conformation of loop 1 and A conformation of loop 2, and we could make this go away by switching A and B in loop 2. I find it to be less confusing if we switch the conformation names in loop 2. What is the consensus view? Tim

2 1

cif_as_mtz assertion error
by Eric Williams 15 Jun '12

15 Jun '12

I'm trying to run phenix.cif_as_mtz on a large number of PDB entries, and several entries give me an assertion error. The example below is from 8icz, but the error always seems to be the same. Traceback (most recent call last): File "/media/funky/phenix-1.8-1069/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/cif_as_mtz.py", line 544, in <module> run(sys.argv[1:]) File "/media/funky/phenix-1.8-1069/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/cif_as_mtz.py", line 135, in run incompatible_flags_to_work_set=command_line.options.incompatible_flags_to_work_set) File "/media/funky/phenix-1.8-1069/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/cif_as_mtz.py", line 197, in process_files r_free_flags = r_free_flags).mtz_object() File "/media/funky/phenix-1.8-1069/cctbx_project/mmtbx/utils.py", line 2001, in __init__ skip_twin_detection = True) File "/media/funky/phenix-1.8-1069/cctbx_project/mmtbx/utils.py", line 2113, in get_r_factor twin_laws = twin_laws) File "/media/funky/phenix-1.8-1069/cctbx_project/mmtbx/utils.py", line 1556, in fmodel_simple assert f_obs.sys_absent_flags().data().count(True)==0 Any ideas? Thanks. :) Eric Williams PhD candidate Intelligent Systems Program University of Pittsburgh

3 8

run time crashing
by CPMAS Chen 15 Jun '12

15 Jun '12

It crashes during rotamer fix at the initial stage. If you like, I can send you the necessary file for you to debugging. > > Message: 7 > Date: Thu, 14 Jun 2012 08:24:44 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] phenixbb Digest, Vol 79, Issue 4 > Message-ID: <4FDA023C.3070306(a)lbl.gov> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hi, > > how long does it take to reproduce this problem in your case? So far I > have examples that take forever before they crash. So if yours takes a > few minutes I would be very interested to have it for debugging. > > Also, Jeff is going to try something else that may eliminate this problem. > > Thanks, > Pavel > > *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

2 1

Re: [phenixbb] phenixbb Digest, Vol 79, Issue 4
by CPMAS Chen 14 Jun '12

14 Jun '12

I thought I am the only one have this problem. I have encountered the same problem with the newest version of phenix. My installation is on MacOS X 10.6.8. If more information needed, I am happy to provide. Traceback (most recent call last): File "/usr/local/phenix-1.8-1069/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/local/phenix-1.8-1069/phenix/phenix/refinement/command_line.py", line 146, in run call_back_handler=call_back_handler) File "/usr/local/phenix-1.8-1069/phenix/phenix/refinement/driver.py", line 1510, in run ncs_manager = self.ncs_manager) File "/usr/local/phenix-1.8-1069/phenix/phenix/refinement/strategies.py", line 575, in refinement_machine log=log) File "/usr/local/phenix-1.8-1069/cctbx_project/mmtbx/torsion_restraints/torsion_ncs.py", line 884, in fix_rotamer_outliers monitor_clashscore=False) File "/usr/local/phenix-1.8-1069/cctbx_project/mmtbx/refinement/real_space.py", line 336, in refine geometry_restraints_manager = geo_box) File "/usr/local/phenix-1.8-1069/cctbx_project/mmtbx/refinement/real_space.py", line 250, in __init__ lbfgs_exception_handling_params = lbfgs_exception_handling_params) File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 137, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/usr/local/phenix-1.8-1069/cctbx_project/scitbx/lbfgs/__init__.py", line 258, in run log) File "/usr/local/phenix-1.8-1069/cctbx_project/scitbx/lbfgs/__init__.py", line 126, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 193, in compute_functional_and_gradients compute_gradients=True) File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/manager.py", line 716, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/manager.py", line 650, in pair_proxies min_cubicle_edge=self.min_cubicle_edge) File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/__init__.py", line 1295, in __init__ shell_asu_tables=shell_asu_tables) RuntimeError: Estimated memory allocation for cubicles exceeds max_number_of_bytes: This may be due to unreasonable parameters: cubicle_edge=5 space_span=(2696.14,2555.98,2650.54) n_cubicles=(540,512,531) max_number_of_bytes=1073741824 > > Message: 1 > Date: Mon, 11 Jun 2012 11:44:07 -0700 > From: Nathaniel Echols <nechols(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] runtime error in phenix.refine > Message-ID: > <CALeAa1PBCCzKPJTMoDsFbsZMSO=SMB_19ns+mfvC3HozuUcBaQ(a)mail.gmail.com > > > Content-Type: text/plain; charset=ISO-8859-1 > > On Sun, Jun 10, 2012 at 10:04 AM, Eugene Valkov <eugene.valkov(a)gmail.com> > wrote: > > I'm encountering the following during the second macro-cycle in > > phenix.refine in latest 1.8-1069 dev build for Linux 64-bit: > > > > RuntimeError: Excessive number of cubicles: > > ?This may be due to unreasonable parameters: > > ? ?cubicle_edge=5 > > ? ?space_span=(8467.78,8440.85,8372.67) > > ? ?n_cubicles=(1694,1689,1675) > > ? ?max_number_of_bytes=101542821888 > > > > Any thoughts/suggestions much appreciated. > > If I'm interpreting the code correctly, this means that the number of > cubicles will lead to an integer format overflow - which I find hard > to believe if you're using a 64-bit system. Could you please send me > the rest of the error message, along with the output of the command > "boost_adaptbx.show_platform_info"? > > thanks, > Nat > > > -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

3 2

Re: [phenixbb] phenixbb Digest, Vol 79, Issue 4
by Kay Diederichs 14 Jun '12

14 Jun '12

"A 64bit operating system" can only run on hardware that supports 64bits. Here, 64bits refers to addresses in memory - arrays larger than 4GB need 64bit addressing because 32bits do not allow high enough numbers to index such arrays. It has nothing to do with the maximum value of an integer - that is set by the programmer. A programmer can (depending on programming language and compiler) usually decide whether integer numbers should be of size 4 bytes or 8 bytes. It is just by coincidence that 8 bytes are 64 bits. Here it seems to me that a 8byte integer would be needed to hold the number of cubicles. best, Kay > Date: Mon, 11 Jun 2012 11:44:07 -0700 > From: Nathaniel Echols<nechols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] runtime error in phenix.refine > Message-ID: > <CALeAa1PBCCzKPJTMoDsFbsZMSO=SMB_19ns+mfvC3HozuUcBaQ(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Sun, Jun 10, 2012 at 10:04 AM, Eugene Valkov<eugene.valkov(a)gmail.com> wrote: >> I'm encountering the following during the second macro-cycle in >> phenix.refine in latest 1.8-1069 dev build for Linux 64-bit: >> >> RuntimeError: Excessive number of cubicles: >> ?This may be due to unreasonable parameters: >> ? ?cubicle_edge=5 >> ? ?space_span=(8467.78,8440.85,8372.67) >> ? ?n_cubicles=(1694,1689,1675) >> ? ?max_number_of_bytes=101542821888 >> >> Any thoughts/suggestions much appreciated. > > If I'm interpreting the code correctly, this means that the number of > cubicles will lead to an integer format overflow - which I find hard > to believe if you're using a 64-bit system. Could you please send me > the rest of the error message, along with the output of the command > "boost_adaptbx.show_platform_info"? > > thanks, > Nat

2 1

MR error when fix one component and search for the other one
by fn1＠rice.edu 13 Jun '12

13 Jun '12

Hi everyone, I am trying to fix one component from the previous MR search and try to search for the other one, euler and frac are taken from the pdb file of the previous run (MR.1.pdb). Here are my input file and error message. Thanks in advance! Fengyun automr { build=false ensemble { ensembleID = "mol1" copies_to_find = 1 coords = in.pdb RMS = 0.85 } ensemble { ensembleID = "mol2" copies_to_find = 0 coords = in.pdb RMS = 0.85 } component { seq_file="mut.seq" component_type = *protein nucleic_acid component_copies = 4 } fixed_ensembles { fixed_ensembleID_list="mol2" fixed_euler_list = 206.66 146.75 96.21 fixed_frac_list = 0.688 1.011 0.005 } } i get the error message like this, ENSEMBLE: mol1 , 1 PDB file(s) ENSEMBLE: mol2 , 1 PDB file(s) Resolution set to 3.5 Specifying composition through protein sequence file /shared.scratch/ni/mut-p222-all/bb-3.5/AutoMR_run_5_/r2/mut.seq 4 Adding Ensemble mol2 as fixed solution with: Euler angles: [206.66, 146.75, 96.21] Coords (orthogonal A): [0.688, 1.011, 0.005] *************ERROR ENDING ******************* **************************************** AutoMR Input failed Python argument types in SOLU.addSOLU_6DIM_ENSE(InputMR_AUTO, str, list, bool, list, float, bool, bool, bool) did not match C++ signature: addSOLU_6DIM_ENSE(phaser::SOLU {lvalue}, std::string, scitbx::vec3<double>, bool, scitbx::vec3<double>, double, bool, bool, bool, bool, scitbx::vec3<double>, double) **************************************** *************ERROR ENDING *******************

2 1

runtime error in phenix.refine
by Eugene Valkov 12 Jun '12

12 Jun '12

I'm encountering the following during the second macro-cycle in phenix.refine in latest 1.8-1069 dev build for Linux 64-bit: RuntimeError: Excessive number of cubicles: This may be due to unreasonable parameters: cubicle_edge=5 space_span=(8467.78,8440.85,8372.67) n_cubicles=(1694,1689,1675) max_number_of_bytes=101542821888 Any thoughts/suggestions much appreciated. Thanks, Eugene -- Dr Eugene Valkov Division of Structural Studies MRC Laboratory of Molecular Biology Hills Road, Cambridge, CB2 0QH Email: evalkov(a)mrc-lmb.cam.ac.uk Tel: +44 (0)1223 402261

3 3

How to run normal mode analysis under command mode?
by fn1＠rice.edu 12 Jun '12

12 Jun '12

Hi everyone, I'd like to perturb my model with normal mode analysis. Does phenix have a way to do this? Thanks in advance! Fengyun

6 11

Gordon conference - last chance!
by Anastassis Perrakis 11 Jun '12

11 Jun '12

Dear all, The registration deadline for the Gordon conference on diffraction methods in Structural Biology (15-20 July), is at the end of the week (June 17th). This is you last chance to register and get some of the places left!!! See the program and application information at: http://www.grc.org/programs.aspx?year=2012&program=diffrac Ana and Tassos

1 0

Ordered solvent DOD
by YoungJin 07 Jun '12

07 Jun '12

Hi, When you add waters by ordered solvent option, is it possible putting DOD for neutron data? I added normal waters and changed them to DOD by using ReadySet. But wondering if I want to go further refinement with ordered_solvent on, how can I keep adding DOD rather than HOH. Otherwise, do I have to change again by using REadySet? I also tried to change resid name as DOD but didn't help me. Best, Young-Jin

3 2

R/Rfree can not be reproduced
by 周文昌 03 Jun '12

03 Jun '12

Dear all, I had a weird case in which I can not reproduce the R/Rfree value for the same refinement. "same" means I run my refinement first and then I rerun with "phenix.refine *.eff --overwrite". The R/Rfree values for the two cases are different (0.2942/0.3190 vs 0.2942/0.3085). Should not they be the same always? the command I used: 1st. phenix.refine new-unique.mtz model.pdb xray_data.high_resolution=2.7 fix_rotamers=true strategy=individual_adp+individual_sites+tls ../tls_group_selections.params wxc_scale=0.05 refinement.input.xray_data.labels=FP,SIGFP --overwrite 2nd phenix.refine model_refine_001.eff --overwrite thanks, Wenchang

3 2

Re: [phenixbb] SA omit map
by Huang, Raven H 02 Jun '12

02 Jun '12

Hi all, Was the issue of SA omit map debated last July (involving Tiaard Pining, Pavel, and Folmer) resolved in the newer version of Phenix? Specifically, We'd like to generate the same map for a ligand. It is not for the refinement, but for publication (a reviewer asked us to cover the ligand with the map in a figure). Previously, I used cns to do that (sa_omit_map.inp). But we refined our current structures solely in Phenix. If there is a choice, I'd rather not to move everything to cns and set it up just for the sake of generating a omit map. Thanks, Raven ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Raven H. Huang, Associate Professor Department of Biochemistry Center for Biophysics & Computational Biology University of Illinois at Urbana-Champaign 411 Roger Adams Lab., 600 S. Mathews Ave. Urbana, IL 61801 Phone: 217-333-3967; Fax: 217-244-5858

3 3

partial partial occupancy
by Terry Lang 02 Jun '12

02 Jun '12

Hey Everyone, I have partially occupied ligand that I am trying model. The problem is that the ligand is in at least two conformations PLUS there is a side chain that occludes binding part of the time. In other words, I'm aiming for something like: Residue Conf A occ = 60%, Residue Conf B occ = 40%, Ligand Conf A 30%, Ligand Conf B 10%. Phenix is happy having a single conformation below 100% occupancy but seems to force the total sum of multiple occupancy residues to be 100%. Is there a way to turn that off for the ligand? Thanks Terry -- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3

2 1

Occupancy refinement
by Jerome Nwachukwu 01 Jun '12

01 Jun '12

Hi: I have a 2.2Å structure containing a ligand in at least 2 alternate conformations. When the structure is refined via XYZ refinement + occupancy using phenix.refine, both ligand conformers are kicked out of the electron density. Is there a way to prevent this? Thank you, -Jerome Sent from my iPhone

3 3

TLS makes my r-factors shoot through the roof
by Morten Groftehauge 30 May '12

30 May '12

Hi Phenixbb, 3.2A data, 110 Wilson B, I41, twinned. Imperfect inverted repeat dsDNA with 4 protein monomers, NCS not used in refinement. If I don't include TLS I get a nice stable R-factor while RMS goes down. If I include TLS (whether as one group per chain or as chosen by Phenix) this happens: [image: Inline images 1] Density disappears around some of the DNA bases as an obvious difference. If I run Refmac with TLS it just never finishes. While I could just refine without TLS this does make me worried that there is something wrong with my model or my data (besides being terrible). Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

2 5

Wilson B and REMARK 3
by Michael Thompson 29 May '12

29 May '12

Hello Everyone, I have a question regarding the Wilson B information reported in REMARK 3 of a pdb file. I am preparing a pdb file for deposition, and I am wondering which is the most appropriate value to report as the Wilson B in REMARK 3? My inclination is to report the Wilson B for the full dataset calculated by XSCALE. This value differs slightly from the Wilson B value calculated by phenix.refine and printed to the refinement log file (XSCALE=27.6 vs. phenix.refine=19.8). I assume this difference is due to phenix.refine using a low-resolution cutoff of ~20A. My concern stems from the fact that REMARK 3 "presents information on refinement program(s) used and the related statistics," so I'm not sure if it's best to include the Wilson B calculated by the refinement software, or the Wilson B for the whole data set. Thanks, Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

2 1

Phenix crashes during refinement of a large structure
by Gino Cingolani 19 May '12

19 May '12

Hi all, PHENIX keeps crashing while refining a large structure (>18,000 residues/asym unit). Can anybody make sense of the following error message (see below)? Thanks so much, Gino ------------------------------------------------------------------------------------------------------------------------------------------------ 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 176, in analyze_clashes stdin_lines=tmp_r.as_pdb_string()) File "/usr/local/phenix-1.7.3-928/cctbx_project/libtbx/easy_run.py", line 147, in __init__ close_fds=not subprocess.mswindows) File "/usr/local/phenix-1.7.3-928/cctbx_project/libtbx/subprocess_with_fixes.py", line 598, in __init__ errread, errwrite) File "/usr/local/phenix-1.7.3-928/cctbx_project/libtbx/subprocess_with_fixes.py", line 1015, in _execute_child self.pid = os.fork() ------------------------------------------------------------------------------------------------------------------------------------------------ ****************************************************************************** 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)

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iterative-build omitmap
by ARJUN＠pitt.edu 18 May '12

18 May '12

Hi I am trying to calculate iterative-build omitmap. Initially program run all 126 omit region and created map coeffs file in corresponding TEMPO subdirectory and unable to create final combined map and this reduce program is running three days without creating the final map. I am trying to run combine_map script separately with all omit region coeffs file and I got the following error: >combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_126 combining map from binary file overall_best_denmod_map_coeffs.mtz_OMIT_REGION_126 >omit Full cross-validation will be done Setting n_small_cycle to 3 All done with inputs Building protein Setting up for building protein Standard fill-in residues: ALA A GLY G Standard main-chain atoms: N CA C O CB All main-chain atoms: N CA C O Max dist between adjacent N atoms: 6.000000 List of all residues: GLY ALA SER VAL ILE LEU MET CYS PHE TYR LYS ARG TRP HIS GLU ASP GLN ASN PRO THR List of 1-letter code of residues: GASVILMCFYKRWHEDQNPT List of number of atoms in side-chains: 0 1 2 3 4 4 4 2 7 8 5 7 10 6 5 4 5 4 3 3 checking license file.. solve2.access The date today is 17-may-12. Your license is good until 15-dec-96. >>>>>> CCP4 library signal library_file:Cannot open file (Error) raised in ccp4_file_open2 <<<<<< >>>>>> CCP4 library signal mtz:Cannot open file (Error) raised in MtzGet <<<<<< Error: failed to open file for read! Sorry, unable to open mtz file: exptl_fobs_phases_freeR_flags.mtz Sorry, unable to open mtz file resolve malloc count: 0 resolve exit_info: How to overcome this error problem Thank you P.Arjunan

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New UPDATE-- Difficult dataset and refinement--P422? I422?Twinning?
by Zhou, Tongqing (NIH/VRC) [E] 17 May '12

17 May '12

Dear All, Kay helped me reprocess the data set with XDS, the program pick up I422 as space group. It turned out that when I originally used XDS, I used spindle axis -1, 0, 0 for the APS ID22 detector, it should be 1, 0, 0. The output from XDS: SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr 8.87 4414 841 858 98.0% 2.7% 3.2% 4402 45.77 3.0% 99.9* -18 0.664 577 6.33 7883 1374 1385 99.2% 3.7% 3.9% 7872 35.76 4.1% 99.9* -17 0.687 1108 5.18 10205 1724 1734 99.4% 5.1% 4.9% 10195 29.38 5.6% 99.8* -15 0.748 1468 4.49 12194 2042 2055 99.4% 5.0% 4.7% 12185 30.77 5.4% 99.8* -20 0.727 1764 4.02 13830 2284 2297 99.4% 6.2% 5.9% 13822 24.55 6.7% 99.8* -15 0.736 2019 3.67 15377 2501 2530 98.9% 9.4% 9.3% 15368 16.77 10.3% 99.6* -12 0.752 2245 3.40 16709 2702 2724 99.2% 14.3% 14.5% 16700 11.31 15.6% 99.2* -5 0.761 2430 3.18 18091 2904 2934 99.0% 23.3% 24.6% 18084 7.14 25.4% 98.4* -3 0.726 2635 3.00 18105 2972 3107 95.7% 37.3% 40.4% 18071 4.42 40.7% 96.4* -6 0.665 2624 total 116808 19344 19624 98.6% 8.2% 8.4% 116699 18.79 9.0% 99.8* -10 0.724 16870 Attached please also find the xtriage log for data processed with XDS. Final model with I422 data set at 3 A resolution looked fine to me, r-free went down from ~0.32 to 0.298, the map even let me correctly fitted one place that supposed to have a Cis-Pro. The final numbers for the model is: r_work = 0.2611 r_free = 0.2983 bonds = 0.002 angles = 0.568 Thank you all for all the help! Regards, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4609B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ****************************************************************** -----Original Message----- From: Pavel Afonine [mailto:[email protected]] Sent: Tuesday, May 08, 2012 2:07 PM To: phenixbb(a)phenix-online.org Subject: Re: [phenixbb] UPDATE-- Difficult dataset and refinement--P422? I422?Twinning? Hi, >> 1. Is it really twinned since including twin-law in refinment gave much >> better numbers? R-factors may not be directly comparable: G.Murshudov, Appl. Comput. Math., V.10, N.2, 2011, pp.250-261. The strategy is: - check to see if Xtriage tells it's twinned (based on reflection statistics, not just predicted twin laws based on geometry); - use phenix.model_vs_data to see if it's worth using it. Pavel _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb

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annealing omit map
by r n 17 May '12

17 May '12

Hi all I have omitted some region manually from the pdb and did annealing - cartesian using phenix.refinment, the resulting map has density (1.2 sigma) in 2fofc and also seen 2.8 sigma negative density on the omitted region? any suggestions? Rab

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Re: [phenixbb] mr.rosetta gui
by Terwilliger, Thomas C 17 May '12

17 May '12

Hi Alex, OK, the problem should be fixed in tomorrow's build. Thank you for pointing it out! Let us know if that does not do it! All the best, Tom T ________________________________ From: Terwilliger, Thomas C Sent: Wednesday, May 16, 2012 10:45 AM To: PHENIX user mailing list Cc: Terwilliger, Thomas C Subject: RE: [phenixbb] mr.rosetta gui Hi Alex, Yes, I can duplicate this...I'm checking on what is happening now. All the best, Tom T ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Alexander Batyuk [batyuk(a)bioc.uzh.ch] Sent: Wednesday, May 16, 2012 1:54 AM To: PHENIX user mailing list Subject: [phenixbb] mr.rosetta gui Dear developers, While trying to run mr.rosetta from the GUI, I've encountered an error (see screenshot). I have un-checked the box Include solvation energy. The file rosetta_weights.wts has been created in WORK_1, fa_sol=0.0. Inspection of mr_rosetta_params.eff in GROUP_OF_PLACE_MODEL_1 revealed include_solvation_energy = False, followed by weights_file = "/Users/abatyuk/Desktop/o1map/MR_ROSETTA_74/WORK_1/rosetta_weights.wts", but it seems that the GUI wants either or. Is that the expected behavior? I'm running 1.8-1056, Rosetta 3.4 on OS X 10.6.8 Best wishes, Alex

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Re: [phenixbb] mr.rosetta gui
by Terwilliger, Thomas C 17 May '12

17 May '12

Hi Alex, Yes, I can duplicate this...I'm checking on what is happening now. All the best, Tom T Dear developers, While trying to run mr.rosetta from the GUI, I've encountered an error (see screenshot). I have un-checked the box Include solvation energy. The file rosetta_weights.wts has been created in WORK_1, fa_sol=0.0. Inspection of mr_rosetta_params.eff in GROUP_OF_PLACE_MODEL_1 revealed include_solvation_energy = False, followed by weights_file = "/Users/abatyuk/Desktop/o1map/MR_ROSETTA_74/WORK_1/rosetta_weights.wts", but it seems that the GUI wants either or. Is that the expected behavior? I'm running 1.8-1056, Rosetta 3.4 on OS X 10.6.8 Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun<http://www.bioc.uzh.ch/plueckthun>

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mr.rosetta gui
by Alexander Batyuk 16 May '12

16 May '12

Dear developers, While trying to run mr.rosetta from the GUI, I've encountered an error (see screenshot). I have un-checked the box Include solvation energy. The file rosetta_weights.wts has been created in WORK_1, fa_sol=0.0. Inspection of mr_rosetta_params.eff in GROUP_OF_PLACE_MODEL_1 revealed include_solvation_energy = False, followed by weights_file = "/Users/abatyuk/Desktop/o1map/MR_ROSETTA_74/WORK_1/rosetta_weights.wts", but it seems that the GUI wants either or. Is that the expected behavior? I'm running 1.8-1056, Rosetta 3.4 on OS X 10.6.8 Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

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Occupancy issue
by Simon Kolstoe 15 May '12

15 May '12

Hi phenixbb, I'm wanting to refine the occupancy for just a few Cadmium atoms in a structure but not refine any other occupancies. I've used the following command however the occupancies haven't refined: phenix.refine refinement_006.def occupancies.individual="chain X and element CD2" and the cadmiums are in the pdb file as: ATOM 8740 CD+2 CD2 X 1 -81.043 91.612 65.218 1.00 11.63 X CD2+ ATOM 8741 CD+2 CD2 X 2 -78.111 92.072 62.948 1.00 11.15 X CD2+ ATOM 8742 CD+2 CD2 X 3 -85.283 28.170 80.931 1.00 12.01 X CD2+ Thanks, Simon

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Refinement error with Se labeled DNA cif seting
by Lauren 15 May '12

15 May '12

Dear all, I have a protein complex with 10mer DNA with one adenine labeled with Se-CH3 at C2'. I gave the se labeled pdb structure to the Elbow or ReadySet, the program gave me the cif as shown below. When I tried to refine the structure, phenix.refine ends with a Error message: Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unexpected atoms: {'AMS,OP1': 1, 'AMS,OP2': 1} Classifications: {'DNA': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Number of atoms with unknown nonbonded energy type symbols: 2 "HETATM 2 OP1 AMS A 1 .*.A O " "HETATM 3 OP2 AMS A 1 .*.A O " Any advice on how to modified the cif or pdb files? Thanks so much in advance. CIF files: AMS P P P . 10.3639 38.8090 53.6083 AMS OP1 O OH1 . 9.8621 39.4308 52.7650 AMS OP2 O O . 9.6270 38.9790 55.3430 AMS O5' O O2 . 11.5188 37.6926 53.7178 AMS C5' C CH2 . 12.2621 37.6244 54.8065 AMS C4' C CR15 . 13.5128 36.9044 54.7141 AMS O4' O O . 14.2653 37.1385 55.8584 AMS C3' C CR15 . 13.2442 35.4155 54.6698 AMS O3' O OH1 . 14.1003 34.8289 53.7923 AMS C2' C CR15 . 13.5010 34.9324 55.9516 AMS SE2' SE SE . 11.8697 34.2402 56.7089 AMS C1' C CR15 . 13.9654 36.1199 56.7679 AMS CA' C CH3 . 11.5566 32.3937 56.0481 AMS N9 N NR5 . 15.1526 35.8937 57.6065 AMS C8 C CR15 . 16.4077 35.6661 57.1789 AMS N7 N N . 17.1943 35.5119 58.2703 AMS C5 C CR56 . 16.4320 35.6429 59.3887 AMS C4 C CR56 . 15.1196 35.8884 58.9705 AMS N1 N N . 15.6651 35.7647 61.7193 AMS C2 C CR16 . 14.4119 35.9994 61.2874 AMS N3 N N . 14.1134 36.0657 59.9478 AMS C6 C CR6 . 16.7122 35.5796 60.8007 AMS N6 N NH2 . 18.1110 35.3174 61.2840 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd AMS P OP1 single 1.162 0.02 AMS P OP2 double 1.892 0.02 AMS P O5' single 1.610 0.02 AMS O5' C5' single 1.320 0.02 AMS C5' C4' single 1.446 0.02 AMS C4' O4' single 1.389 0.02 AMS C4' C3' single 1.514 0.02 AMS O4' C1' single 1.398 0.02 AMS C3' O3' single 1.359 0.02 AMS C3' C2' single 1.394 0.02 AMS C2' SE2' single 1.927 0.02 AMS C2' C1' single 1.514 0.02 AMS SE2' CA' single 1.986 0.02 AMS C1' N9 single 1.471 0.02 AMS N9 C8 aromatic 1.345 0.02 AMS N9 C4 aromatic 1.364 0.02 AMS C8 N7 aromatic 1.354 0.02 AMS N7 C5 aromatic 1.360 0.02 AMS C5 C4 aromatic 1.399 0.02 AMS C5 C6 aromatic 1.441 0.02 AMS C4 N3 aromatic 1.414 0.02 AMS N1 C2 aromatic 1.346 0.02 AMS N1 C6 aromatic 1.405 0.02 AMS C2 N3 aromatic 1.374 0.02 AMS C6 N6 single 1.503 0.02 Best Regards Lauren

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refinement of peptide with non-standard aminocids
by Vitali Stanevich 15 May '12

15 May '12

Hi, I am trying to refine protein structure with MCLR ligand - this is cyclic hepta-peptide which has some non-standard amino acids. Sequence is DAL-LEU-ACB-ARG-1ZN-FGA-DAM. It's exactly the same compound as chain G at 3dw8 PDB entry. I could successfully import amino acids in coot through "get monomer" option, renumber and combine in one chain. Problem is that whenever I use phenix.refine it returns all residues nonbonded. Corresponding carboxyl and amino groups are in close proximity to make a bond. I tried to write LINKR record in .pdb - with no success: ... LINKR 1ZN G 5 FGA G 6 trans LINKR FGA G 6 DAM G 7 trans ... Is there a way to create peptide bonds in this inhibitor chain? I'm using phenix Version: 1.7.3. Thanks in advance, Vitali

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