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Job Opportunity - Head of the Berkeley Center for Structural Biology
by Paul Adams 04 Dec '11

04 Dec '11

The Physical Biosciences Division at Lawrence Berkeley National Laboratory is seeking candidates for the Head of the Berkeley Center for Structural Biology. This position provides scientific, technical and operational oversight of the BCSB at the Advanced Light Source (ALS), a third generation synchrotron facility. The BCSB is a user resource for structural biology experiments and consists of 5 beamlines at 2 sectors of the ALS, with a staff of 16. This Staff Scientist position will provide leadership and direction to develop methodology and instrumentation for collecting and analyzing crystallographic data using synchrotron radiation, and on projects involving the structure determination of biological molecules using X-ray crystallography. This position focuses on the field of crystallography, and involves interactions and collaborations with researchers from multiple scientific disciplines including chemistry, crystallography, biochemistry, biology, physics and computational sciences. For full details please visit the job application link at: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=73970 Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 13 Nobel Prize recipients over the past 75 years. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/EEO employer committed to the development of a safe and diverse workforce. Learn more about the Lab at http://www.lbl.gov. -- 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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pdb hierarchy
by Bradley Hintze 03 Dec '11

03 Dec '11

Hi Phenix, I have a hierarchy question. I was using the hierarchy and got something that I did not expect. when running this: pdb_io = pdb.input(pdbfile) hierarchy = pdb_io.construct_hierarchy() for model in hierarchy.models(): print model.id for chain in model.chains(): print ' ' + chain.id When I do this I expect the chains in pdbfile to be printed once for each model in pdbfile. However, when I ran this I got, for example, chain 'A' printed four times under the same model. Why is this? Thanks, Bradley

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Writing PDB
by Bradley Hintze 03 Dec '11

03 Dec '11

Hi again, I am trying to take a pdb and write out a new pdb with just a specified chain. I am trying to do this with the hierarchy but am unfamiliar with its functions How do I do this? Thanks, Bradley

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the Ming dial
by Dialing Pretty 03 Dec '11

03 Dec '11

Dear All, In the Ming dial, there is a occupancy (%), which indication of excellent , good, etc. Does it mean if I choose the "occupancy" of excellent, the rotamer outlier ratio will be lowered? My crystal has a resolution of 2.8, and I find no matter how I turn the dial, the original fits the map best. Currently my rotamer outlier is 8%, thus I need the way to have it solved. In addition, for Coot and Ming, which is much convenient to reduce rotamer outlier? I am looking forward to getting your reply. Cheers, Fenghui

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on the rotamer optimization
by Dialing Pretty 03 Dec '11

03 Dec '11

Dear All, Besides Coot and Ming, is any software or server which could further optimize the side chain outliers? I am looking forward to getting your reply. Cheers, Dialing

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solvent model in phenix.refine
by Weiergräber, Oliver H. 01 Dec '11

01 Dec '11

Hello, the ordered_solvent option in phenix.refine apparently uses these parameters by default: min_model_peak_dist = 1.8 max_model_peak_dist = 6.0 min_peak_peak_dist = 1.8 I was wondering about the justification for this (extremely relaxed) set of limits. As far as I know, the shortest hydrogen bonds (if defined as donor-acceptor distance) are about 2 A, and even these are considered exceptional and rare. Similarly, anything in excess of 3.5 A is quite unlikely to be significant energetically, so why use 6 A as an upper limit? Even if max_model_peak_dist was only meant to limit the extent of the outer solvent shell, there is no such thing as max_peak_peak_dist to avoid unreasonably long individual bonds. My personal suggestion would be a range of about 2.3 - 3.2 A for a significant hydrogen bond, with the lower limit exemplified by charged interactions (carboxyl-water or oxonium-water), which tend to be shorter - and stronger - than average. On the other hand, I do frequently observe elongated densities which, in accordance with the default parameters, are typically interpreted by phenix.refine as two water molecules about 2 A apart. So the question arises whether this is a realistic assumption, compared to a "sliding water" model in which the position of a single molecule is just ill-defined in a certain direction (due to a competition of adjacent binding sites for example)? Best regards, Oliver ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-1448 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Clashing alternative conformations
by Sozanne Solmaz 01 Dec '11

01 Dec '11

Dear all, I have the following problem: I have a homodimer of two protein chains A and B, which I refine in Phenix, and one residue has 2 alternate conformations (a and b) for each chain. If the residues of both chains A and B are in the alternative conformation b, they clash. However, I would expect that never both residues are in conformation b, and therefore only the combinations aa, ab and ba of alternative conformations exist. My problem is, that during the refinement, the two b conformations of the residues clash, which drives the clash-score of the overall structure to a very high value and repulsion pushes the two b-conformations apart during refinement, therefore I cannot model them properly. Is it possible in Phenix to define these two conformations as non-clashing and non-repulsive? Thank you, best regards, Sozanne Solmaz.

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"nproc" in phenix.refine
by Jonathan Elegheert 30 Nov '11

30 Nov '11

Dear all, I have a question regarding the "nproc" parameter in phenix.refine; We have the software installed on our university HPC cluster, which has nodes built up of 8 processors each. Submission works via a queuing system ("qsub"). I understand that compiling with OpenMP renders the nproc parameter disfunctional. Does this then imply that I will be limited to 1 node (8 processors) if compiled without OpenMP, since there is no "message passing" to other nodes? Or is there a way to make use of more of the available nodes, for example by compiling with OpenMP and then specifying many nodes with 1 processor? Best regards, Jonathan Elegheert PhD Student Unit for Structural Biology & Biophysics Ghent University jonathan.elegheert(a)ugent.be

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Nitric Oxide ligand keeps getting pushed far away from specified links in CIF
by Yarrow Madrona 29 Nov '11

29 Nov '11

Hello, I am having some trouble refining a structure with Nitric Oxide coordinated to the Heme Fe. I attempted to merge two Cif files. One for another ligand (CNL) and one for NO (NO.cif). I have saved the merged file as CinNO2.cif. In the defualt refinement I type the following into the command line: Mymodel.mtz mymodel.pdb CinNO2.cif Phenix refine runs fine without any errors but pushes the NO much further than the 1.9 angstrom specified by the links in the cif file. I have pasted the contents of the cif file below. The NO, Fe links are at the end of the file. Thank you for any help you can provide. -Yarrow # Files merged : Tue Oct 4 10:11:22 2011 # # CNL.cif # NO.cif # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level CNL CNL Unknown ligand 29 11 . NO NO Unknown ligand 2 2 . # data_comp_CNL # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z CNL C1 C CT . 55.3085 -9.1280 -43.0216 CNL C2 C CH2 . 55.6432 -10.5699 -43.1750 CNL C3 C CH2 . 54.6509 -11.3139 -43.9725 CNL C4 C CH1 . 53.4902 -10.4784 -44.3504 CNL C5 C CH2 . 53.9278 -9.3349 -45.0693 CNL C6 C CH2 . 54.8932 -8.4964 -44.3064 CNL C7 C CH3 . 56.3801 -8.3679 -42.3275 CNL C8 C CT . 52.9353 -9.9244 -43.0573 CNL C9 C CH3 . 52.3495 -11.0301 -42.2453 CNL C10 C CH3 . 51.8314 -8.9341 -43.2982 CNL O O O2 . 54.1049 -9.2461 -42.2221 # 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 CNL C1 C2 single 1.488 0.020 CNL C1 C6 single 1.491 0.020 CNL C1 C7 single 1.486 0.020 CNL C1 O single 1.450 0.020 CNL C2 C3 single 1.475 0.020 CNL C3 C4 single 1.479 0.020 CNL C4 C5 single 1.420 0.020 CNL C4 C8 single 1.512 0.020 CNL C5 C6 single 1.489 0.020 CNL C8 C9 single 1.492 0.020 CNL C8 C10 single 1.502 0.020 CNL C8 O single 1.589 0.020 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd CNL C3 C2 C1 113.16 3.000 CNL C5 C6 C1 112.56 3.000 CNL C8 O C1 110.85 3.000 CNL C6 C1 C2 112.60 3.000 CNL C7 C1 C2 112.43 3.000 CNL O C1 C2 99.48 3.000 CNL C4 C3 C2 112.41 3.000 CNL C5 C4 C3 110.02 3.000 CNL C8 C4 C3 106.05 3.000 CNL C6 C5 C4 113.20 3.000 CNL C9 C8 C4 109.75 3.000 CNL C10 C8 C4 111.96 3.000 CNL O C8 C4 109.61 3.000 CNL C8 C4 C5 104.53 3.000 CNL C7 C1 C6 112.76 3.000 CNL O C1 C6 106.18 3.000 CNL O C1 C7 112.51 3.000 CNL C10 C8 C9 106.70 3.000 CNL O C8 C9 108.62 3.000 CNL O C8 C10 110.10 3.000 # loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period CNL Var_01 C4 C8 O C1 10.40 30.0 3 CNL Var_02 C9 C8 O C1 130.31 30.0 3 CNL Var_03 C10 C8 O C1 -113.19 30.0 3 # loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign CNL chir_01 C1 C6 C7 O both CNL chir_02 C4 C3 C5 C8 both # data_comp__NO # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z NO N N N . -5.7690 4.3760 32.3600 NO O O O . -4.8990 5.2460 32.3600 # 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 NO N O double 1.150 0.02 # data_link_list loop_ _chem_link.id _chem_link.comp_id_1 _chem_link.mod_id_1 _chem_link.group_comp_1 _chem_link.comp_id_2 _chem_link.mod_id_2 _chem_link.group_comp_2 _chem_link.name HEM-CYS HEM . . CYS . . bond_CYS-SG_=_HEM-FE NO -HEM HEM . . NO . . bond_HEM-FE_=_NO-N # data_link_HEM-CYS # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd HEM-CYS 1 FE 2 SG . 2.300000 0.020 # loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd HEM-CYS 2 SG 1 FE 1 NC 109.471221 3.000 HEM-CYS 1 FE 2 SG 2 CB 109.471221 3.000 # data_link_NO -HEM # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd NO -HEM 1 N 2 FE . 1.900000 0.020 # loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd NO -HEM 2 FE 1 N 1 O 140 3.000 NO -HEM 1 N 2 FE 2 NC 103 3.000 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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Mn - O distances
by Timothy Springer 29 Nov '11

29 Nov '11

Hi, We are refining structures with Ca binding sites that are replaced by Mn. Using the coordination restraints in Phenix (distance only) obtained with phenix.metal_coordination, we wind up with the ligands coming somewhat too close, so there is positive density on the opposite side of the ligating residue from the metal. We may have a series of problems, including incomplete replacement of Ca by Mn. However, the bigger issue I want to address is coordination number. In the work by Shannon and Prewitt, such as Acta Cryst. B25, 925, metal oxides are examined, and the point is made that the Mn-O distance with a coordination number of 6 is shorter than for 7. Ca commonly has either 6 or 7 ligands, and with 7 ligands (most common) the O cannot squeeze as tightly together and are farther away from Ca. Mn more commonly has 6 ligands, but can have 7. What are the distance restraints in Phenix based on? They seem similar to those in Harding MM, Acta Cryst D62, 678 (2006). This paper lumps measurements for different coordination numbers together for Mn-O and Ca-O distances, but not for Co, Cu, and Zn. It does seem to help to add metal ion restraints in Phenix. Things don't seem to come out as well without them. Would it be helpful to treat 6 and 7-coordinate metals differently? Or should we just loosen the restraints? How does Refmac treat metals? One does not need to add restraints in its case. With my best regards, Tim Timothy A. Springer, Ph.D. Latham Family Professor of Biological Chemistry and Molecular Pharmacology Harvard Medical School http://idi.harvard.edu/springer Immune Disease Institute springer(a)idi.harvard.edu Program in Cellular and Molecular Medicine, Dept. Medicine Div. Hematology Children's Hospital Boston 3 Blackfan Circle, Rm 3103 phone: 617-713-8200 Boston MA 02115 fax: 617-713-8232

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Metal restraints at special position
by Yuri 28 Nov '11

28 Nov '11

I have a Mg2+ coordinated to 4 waters and 2 side chains. Some of the waters are at special postions. I generated the restraints file using "phenix.metal_cordination input.pdb" When I run refine with my .edits restraints file it crashes due to the special position. How do I handle this? Best, -- Yuri Pompeu

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phenix-1.7.2-x refine error
by Christoph Parthier 25 Nov '11

25 Nov '11

Dear Phenix developers, Using the current phenix version, refinements of a 'certain structure' always stop with the error message quoted below, while the refinement of other 'similar structures' work flawlessly. In the error case the three scheduled macrocycles of refinement seem to finish (the refined PDB is there) but at there seems to be problem in finishing the job - the output MTZ file has zero byte length and the last line in refine.log is: ============================== Exporting results ============================== This occurs with several 1.7.2-x versions of phenix, I'm not sure about 1.7.1-x. Interestingly, the 'problem structure' can be refined without problems using the same input files in phenix-1.7-650. Any idea whether this is due to an installation problem or a bug? Thanks, Christoph Here's the error message: MemoryError : Traceback: File "/cryst/phenix-1.7.2-869/cctbx_project/libtbx/thread_utils.py", line 229, in run return_value = self._target(self._args, self._kwargs, self._c) File "/cryst/phenix-1.7.2-869/cctbx_project/libtbx/runtime_utils.py", line 72, in __call__ result = self.target() File "/cryst/phenix-1.7.2-869/phenix/phenix/refinement/runtime.py", line 67, in __call__ call_back_handler=callback) File "/cryst/phenix-1.7.2-869/phenix/phenix/refinement/command_line.py", line 115, in run map_manger.write_files() File "/cryst/phenix-1.7.2-869/phenix/phenix/refinement/driver.py", line 1535, in write_files map_coeff_dataset=self.write_mtz_file(), File "/cryst/phenix-1.7.2-869/phenix/phenix/refinement/driver.py", line 1524, in write_mtz_file params = self.map_params.map_coefficients) File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/maps/__init__.py", line 502, in __init__ coeffs = map_coefficients_from_fmodel(fmodel = fmodel, params = mcp) File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/maps/__init__.py", line 353, in map_coefficients_from_fmodel fill_mode = "dfmodel") File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/f_model.py", line 1887, in electron_density_map fill_mode = fill_mode) File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/map_tools.py", line 114, in __init__ update_scaling = update_scaling) File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/f_model.py", line 1663, in fill_missing_f_obs fmodel=self, fill_mode=fill_mode, update_scaling=update_scaling) File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/missing_reflections_handler.py", line 131, in fill_missing_f_obs fmodel = select_by_map_cc(fmodel = fmodel.deep_copy())) File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/missing_reflections_handler.py", line 85, in select_by_map_cc fourier_coefficients = coeffs) File "/cryst/phenix-1.7.2-869/cctbx_project/cctbx/miller/__init__.py", line 3688, in __init__ conjugate_flag=True) Platform info: __FILE__ = /net/longnose/scratch2/phenix/phenix-1.7.2-869/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = Sep 23 2011 __TIME__ = 00:13:14 __i386__ __linux __GNUC__ = 3 __GNUC_MINOR__ = 4 __GNUC_PATCHLEVEL__ = 2 boost::python::cxxabi_cxa_demangle_is_broken(): false __GXX_WEAK__ = 1 __VERSION__ = 3.4.2 20041017 (Red Hat 3.4.2-6.fc3) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 61 BOOST_LIB_VERSION = 1_48 PY_VERSION = 2.7.2 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 4 sizeof(std::size_t) = 4 sizeof(void*) = 4 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 12 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 gnu libc version: 2.6.1 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED os.name: posix sys.platform: linux2 sys.byteorder: little platform.platform(): Linux-2.6.22.13-GOLIAT-0.3-bigsmp-i686-with-SuSE-10.3-i586 platform.architecture(): ('32bit', 'ELF') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 8 Memory total: 4,238,028,800 Memory free: 3,715,174,400 import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00'] u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = Ã

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回复：phenixbb Digest, Vol 72, Issue 10
by dingding830106＠sina.com 24 Nov '11

24 Nov '11

Dear Thomas: I try running phenix.autosol instead of phenix.solve, and it solve this problem. Thanks a lot! Dingwei ----- 原始邮件 ----- 发件人：phenixbb-request(a)phenix-online.org 收件人：phenixbb(a)phenix-online.org 主题：phenixbb Digest, Vol 72, Issue 10 日期：2011年11月23日 01点08分 Message: 14 Date: Tue, 22 Nov 2011 10:08:46 -0700 (MST) From: "Thomas C. Terwilliger" <terwilliger(a)lanl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Subject: Re: [phenixbb] solve/resolve problem Message-ID: <52791.128.165.72.7.1321981726.squirrel(a)webmail.lanl.gov> Content-Type: text/plain;charset=iso-8859-1 I'm sorry for the problem! I don't recognize this error (the message solve is giving you is just saying that it has finished, unfortunately). Can you possibly (off-list) send me your input script and the output log file and I'll have a look? Or even better, try running phenix.autosol on the data and perhaps that will solve the problem! All the best, Tom T >> >> >> Dear all >> when I use SOLVE to deal with the SAD data, it will stop with a error >> message: >> >> ???STOP at >> /net/longnose/scratch2/phenix/phenix-1.7.2-869/solve_resolve/solve/solve_2.cpp(3133)??? >> Can you tell me what happen? >> >> wding >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb

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measuring angle
by Hena Dutta 23 Nov '11

23 Nov '11

Hi, Could you please tell me how I can measure angle between two helices. Can COOT or PYMOL measure this? I have another question. In PDBSET, I can use CHAIN command in shell script to write a pdb file with a desired chain ID. What is the command in shell script to write a pdb file with a desired SEGID? As for example:- pdbset xyzin start.pdb xyzout end.pdb <<eof >& pdbset.log ROTATE [INVERT] [MATRIX] values CHAIN A end eof This will change the chain ID to A after rotation. But, I also like to give a segid in the end coordinate. Thank you in advance and have a nice THANKS GIVING WEEKEND Hena

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reference model restrain error
by Stephan Barden 23 Nov '11

23 Nov '11

Dear all, I'm facing a problem with a fresh (yesterday) installation of phenix 1.7.2-869 refining a structure with 6 molecules per ASU at 3.25 A and using a different reference structure with 1 mol/ASU at higher resolution. I wrote an additional parameter file to assign the reference model to each of the six molecules, which worked well with an older version of phenix. After the upgrade neither taking the additional parameter file, nor auto alignment worked for me. The error comming up is always: RuntimeError : Duplicate sequence number and insertion code. Traceback: File "/sw/phenix-1.7.2-869/cctbx_project/libtbx/thread_utils.py", line 229, in run return_value = self._target(self._args, self._kwargs, self._c) File "/sw/phenix-1.7.2-869/cctbx_project/libtbx/runtime_utils.py", line 72, in __call__ result = self.target() File "/sw/phenix-1.7.2-869/phenix/phenix/refinement/runtime.py", line 67, in __call__ call_back_handler=callback) File "/sw/phenix-1.7.2-869/phenix/phenix/refinement/command_line.py", line 75, in run overwrite = command_line_interpreter.command_line.options.overwrite) File "/sw/phenix-1.7.2-869/phenix/phenix/refinement/driver.py", line 209, in __init__ log=self.log) File "/sw/phenix-1.7.2-869/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 145, in __init__ self.get_reference_dihedral_proxies() File "/sw/phenix-1.7.2-869/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 611, in get_reference_dihedral_proxies log=self.log) File "/sw/phenix-1.7.2-869/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 398, in process_reference_groups raise e Has anyone observed a similar problem? Are there any suggestions? Thanks, StephanB.

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solve/resolve problem
by dingding830106＠sina.com 22 Nov '11

22 Nov '11

Dear all when I use SOLVE to deal with the SAD data, it will stop with a error message: “STOP at /net/longnose/scratch2/phenix/phenix-1.7.2-869/solve_resolve/solve/solve_2.cpp(3133)” Can you tell me what happen? wding

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How to reduce clashscore value
by CelinaSocek 21 Nov '11

21 Nov '11

Hi all, I'm now using phenix to refine a small protein about 300 residues long. The resolution of my data is about 2.9 angstrom. Currently I got a refined model with good R-factors about 23/26, RMSD very reasonable and no Ramanchandran outliers. However, I found that the clashscore is extremely high: 63!! And rotamer outliers are also a lot: 8.5%. I wonder, what kind of stretagy I can use to reduce this? Thank you very much! best, Celina

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test_hhr
by Alexander Batyuk 21 Nov '11

21 Nov '11

Dear all, The phenix_regression.wizards.test_command_line_rosetta_quick_tests command hangs at the test_hhr step in phenix-dev-910 on Mac OS X 10.6.8. What could be the reason for that? What kind of log files should I post? The firewall allowed to fetch files from the net. Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

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Re: [phenixbb] How to reduce clashscore value
by CelinaSocek 20 Nov '11

20 Nov '11

Thank you Nat! I will try to fix as many clashes as I can in coot, and hope that I can manage to reduce it to around 20. ;) Also thank other suggestions and discussions! best, Celina > > Which version are you using? We made some changes over the summer > that improve the geometry, especially the clashscore - these are > present in version 1.7.2. If you're still using an earlier version, > this might largely fix the problem. However, if there is > conformational strain in the model, it is difficult to fix severe > clashes without further rebuilding. You should inspect the clashes in > Coot (the Phenix GUI has shortcuts for this, but Coot alone also has > this capability) and fix as many as possible yourself. It is > recommended that you use explicit hydrogen atoms when doing this, > since the reason for clashes is often not obvious if only heavy atoms > are used. (You don't necessarily need to refine with heavy atoms > though - they're just an aid to visualizing clashes.) > > The rotamer problem may be related; there isn't much you can do with > these except fix them manually, but relieving some of the clashes may > help. The dihedral angle restraints simply aren't that strong, so in > areas of weak density it can be difficult to completely prevent > outliers. > > -Nat > > > ------------------------------ > >

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multiple ligand conformations
by Leonard Thomas 19 Nov '11

19 Nov '11

Hello All, One of the groups here has run into a problem in the refinement of their structure or more specifically a ligand bound to the structure. Through a series of other experiments they know that a photo reaction occurs to the compound when exposed to high flux as found at your everyday synchrotron source. The exposure changes the bonding such that there are two conformations with a bit in between obviously. They collected 360 degrees worth of data and if the data is split you can model the two conformations depending which half of the data you use. They are trying to refine with all of the data and modeling of the ligand into the two conformations. In refmac they can model this with no problem but in Phenix the ligand adopts a chemically wrong conformation, sort of a halfway point between the two chemically relevant conformations. They have used Phenix to do similar refinements on other structures but it appears either the last release or the latest release is causing problems. They have started out with everything from 50% occupancy to shifting it towards on one conformation or the other and the ligand always ends up in the chemically wrong position. Data is in the 1.4-1.5 ang. range. Ideas? Thanks in advance. Len Leonard Thomas Ph.D. Macromolecular Crystallography Laboratory Manager University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 lmthomas(a)ou.edu http://barlywine.chem.ou.edu Office: (405)325-1126 Lab: (405)325-7571

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multiple ligand conformations
by Yuri 19 Nov '11

19 Nov '11

Hi, When you say "wrong postion", what does it mean? are the 2 ligands you are trying to refine being "pushed away" from each other? If that is the case first thing I would check is the ALTLOC comlumn of their pdb file entries. Make sure one is ALTLOC A and the other ALTLOC B. I have refined with ligands in four different positions before using phenix before and got satisfactory results... Hope this helps, -- Yuri Pompeu

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MR_ROSETTA
by Wei Shi 18 Nov '11

18 Nov '11

Hi all, I am trying to run phenix.mr_rosetta using the following script for rebuilding the model with Rosetta before MR from phenix website except omitting specifying ncs_copies number. Following is the script I am using: phenix.mr_rosetta \ seq_file = seq.dat \ data=coords1.mtz \ search_models=coords1.pdb \ run_prerefine=True \ number_of_prerefine_models=1000 \ fragment_files = test3.gz \ fragment_files = test9.gz \ rescore_mr.relax=False \ rosetta_models=20 \ space_group=p222 \ use_all_plausible_sg=False \ nproc=4 \ group_run_command=qsub\ When I run the above script, it gives the following error message: child process stderr output: command: 'qsub /home/wei/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1' /bin/sh: qsub: not found Then, I omit the last line in the command “group_run_command=qsub\”. MR_ROSETTA seems to be running. But, it takes forever to run. My questions is: 1. Does anyone happen to know why it tells me “qsub: not found” when I include “group_run_command=qsub” in my script? 2. When I omit “group_run_command=qsub” in the script, mr_rosetta seems to be running. But it just gives me the following message and it takes forever to run. Almost 10h later, no job is finished. I don’t know whether this is normal. If not, any idea about why it’s so slow and any suggestions about how to speed up the run? Thank you so much! Splitting work into 1 jobs and running with 4 processors using sh background=True in /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1 Starting job 1...Log will be: /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log

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error: Duplicate selections
by Sebastiano Pasqualato 16 Nov '11

16 Nov '11

Hi all, sorry guys, this might be a silly one, but I can't see where I'm making the mistake. Whenever I turn on TLS refinement, I get this error message. And, as you can see, the Log file doesn't tell me much more. I have generated the TLS groups wit the 'TLS groups selection' tool in phenix. Any hint? Thanks in advance, ciao s -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990

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Scattering from riding hydrogens?
by Damian Ekiert 15 Nov '11

15 Nov '11

Hello, I have a question regarding two parameters and how they affect riding hydrogens. contribute_to_f_calc = True high_resolution_limit_to_include_scattering_from_h = 1.6 At lower resolution, setting contribute_to_f_calc = false is frequently helpful when using riding hydrogens and has been discussed before. But what is high_resolution_limit_to_include_scattering_from_h = 1.6 doing? If scattering from hydrogens is only included at higher than 1.6A resolution, it would seem like contribute_to_f_calc = True/False would not have any effect at say, 3.5A, but comparing identical refinement runs with contribute_to_f_calc = True or contribute_to_f_calc = False clearly gives different results. Can hydrogens contribute to Fcalc in a way aside from their scattering, or is their contribution accounted for independent of the position of the riding hydrogen (e.g., additional scattering term added to the associated heavy atom)? I think I am misunderstanding what these two parameters are doing and would appreciate some clarification. Thanks, Damian Ekiert

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Multiple TLS groups per molecule
by Yarrow Madrona 15 Nov '11

15 Nov '11

Hi, I would like run TLS and individual isotropic refinement. I want to separate one molecule into four TLS groups. I havn't found documentation for this. Is the number of TLS groups automatically done by phenix refine when you tell it to run TLS refinement on the whole molecule? Thanks for your help -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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