November 2011 - phenixbb - phenix-online.org

Problem with version 1.7.1-743 on OSX
by Miguel Ortiz Lombardía 06 Feb '12

06 Feb '12

Dear phenix developers, Last Friday (April 29) we upgraded phenix to its most recent version (1.7.1-743). Installation went smoothly on both Mac (10.6.7 64-bit) and Linux (Ubuntu 10.10 64-bit) machines. However, we observe that we cannot use phenix.refine (I don't know for the rest of the applications) from the GUI on the Macs. phenix.refine does work from the command line, though. So, whenever we try to add a pdb in the GUI, we get this error message: This application does not support the file type for /path/to/the/file.pdb (format: txt) If we try to open an mtz, it sometime works, but most often we get: PHENIX did not recognize the file type for /path/to/the/file.mtz! and on the terminal from where the GUI was started we can find: **SYMMETRY OPERATOR ERROR** Error in interpreting symop " X+2/3, Y+1/3, Z+1/3 " **SYMMETRY OPERATOR ERROR** Error in interpreting symop " -Y+2/3, X-Y+1/3, Z+1/3 " (and so on, so forth). Any clues ? Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:[email protected] http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Chirality of Ribityl chain of FMN inverted
by Yuri 09 Jan '12

09 Jan '12

Hello Developers, When I built Ligand restraints using eLBOW, my resulting .pdb had an inverted chiral center in the ribityl chain of the flavin mononucleotide particularly C4'. In the database the ligand had an S configuration (correct), but after minimization and restraint generation the output had R configuration at that particular center. I wonder if there is a way to enforce the configuration for each center, although I suspect it could be a little bug, because I noticed my restraints have that center annotated as S eventhough it is R in the actual .pdb Cheers, -- Yuri Pompeu

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AutoBuild Question
by Page, Rebecca 12 Dec '11

12 Dec '11

Dear phenix community: I ran AutoBuild.dat with a seq.dat file that has 3 separate sequences. Chains A and B were built, but chain C was not, even though there is density for the third chain. It occurred to me that only two of the three chains may have been read in. I seem to recall that seq.dat can be a maximum of two sequences, but am not sure. So, is there a limit to the number of sequences that can be present in seq.dat and if so, what is the limit. Thanks in advance, Rebecca

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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 30 Nov '11

30 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 30 Nov '11

30 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 29 Nov '11

29 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 25 Nov '11

25 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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