======================================================================= = = = Crystallography & NMR System = = = = A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, = = R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, = = N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warren = = = = Copyright (c) 1997-2007 Yale University = = = ======================================================================= Program: CNSsolve Version: 1.2 Patch level: 0 Status: general release Changes for version 1.2 ----------------------- Program: - default number of atoms set to 200,000 - atom number can go up to 999999 in the PDB files produced by CNS by using some of the 'ATOM' and 'HETATM' record if the number goes above 99999 - fixed bug in treatment of HL coefficients for remapping of reflections for some spacegroups - installation files for x86_64 linux platforms (using gfortran or ifort) - installation files for Intel Mac systems (using ifort) - installation files for Mac PPC systems - Intel Mac OSX binary distribution - all known dynamic memory pointer problems fixed - Windows binary installation removed - use of sort function updated in cns_solve_env file - use of sed updated in cns_solve_env file - consolidated distribution into one tar file - updated output files in the test directory - generic CPU_TIME subroutine call for Intel Mac OSX, Intel X86_64, and Intel i686 - replaced -tpp7 option with -axP for Intel X86_64 and Intel i686 - removed "norm" function from atom property do command - enabled DISP=KEEP for CLOSe statement on linux and mac intel versions Task files: - updated bulk solvent model and scale factor calculations (developed for robust refinement and low resolution applications): all refinement and model map task files: - new solvent model grid search and solrad/shrink search - absolute grid size range for solvent mask calculation is forced to be between [sqrt 3*0.577 = 1] 0.57 and 0.9 A - removed low_res_bscale parameter, the low resolution limit is used - reported anisotropic tensor in coordinate files is now Ucart (not Ucif as before) - fixed anisostropic B-scaling symmetry restraints in all modules (scalef, - removed "anisotropic_fixed_isotropic" option throughout all script files - fixed method to remove isotropic component from anisotropic B-tensor - new bulk solvent and scaling routines in structure deposition files: xtal_pdbsubmission/xtal_pdbsubmission.inp xtal_mmcif/deposit_mmcif.inp - fixed bug when a structure has a lower resolution that th default Wilson limit: xtal_pdbsubmission/xtal_pdbsubmission.inp - automatic and fixed bulk solvent parameter options: all refinement and model map task files - new automatic sharpening B-factor determination script file: xtal_util/bsharp.inp - B-sharpening parameter introduced into various map files: xtal_util/fourier_map.inp xtal_refine/model_map.inp sa_omit_map.inp composite_omit_map.inp fo-fo_map.inp - corrected local real space correlation coefficient computation: xtal_refine/model_map.inp composite_omit_map.inp water_delete.inp xtal_twin/model_map_twin.inp - fixed Wilson calculation for very large structures xtal_util/bsharp.inp analyse.inp scale.inp - fixed bug in water picking if no sites are found: xtal_refine/water_pick.inp xtal_twin/water_pick_twin.inp - duplicate water parameters no longer read in water picking: xtal_refine/water_pick.inp xtal_twin/water_pick_twin.inp - introduced optional B-factor reset option: xtal_refine/refine.inp - increased the default number of cycles to 3: xtal_refine/refine.inp - removed multiple coordinate file reading option: xtal_refine/composite_omit_map.inp sa_omit_map.inp model_map.inp xtal_util/model_phase.inp xtal_twin/model_map_twin.inp - removed option to write separate bulk solvent model structure factors: xtal_util/model_phase.inp - increased the default number of macrocycles to 15: xtal_phase/mad_phase.inp - changed the default output array name to fmodel and added warning if fcalc is used as the name: xtal_util/model_fcalc.inp - increased maxtree to 20: in all torsion angle input files - Ucart reported instead of Ucif: heavy atom site refinement scripts - modified Patterson map task files to use ascii map files instead of binary map files: xtal_patterson/predict_patterson.inp patterson_map.inp - updated density_modify.inp task file: mask completion warning about absolute scaling of input amplitudes - new input file to calculate structure factors from an EM reconstruction map: xtal_util/em_map_to_hkl.inp HTML Documentation: - updated installation documentation Modules: - fixed bug in siterefine module: FOMs for centrics were non-zero for SAD phasing - removed "anisotropic_fixed_isotropic" option throughout all modules: scaleftarget, scaleftarget2, scale_and_solvent - new module: scale_solvent - new module for automatic determination of FFT gridding parameters fft_parameter_check: - determines optimum B-factor increment - ELIM parameter is automatically increased for atomic resolution structures (starting at 1.4 A and higher) - default ELIM value is set to 8 - grid size is set to the min of ( 1, d_min * 0.3333 ) Libraries: - conformational database library files incorporated into distriubtion libraries/confdb/* Utilities: - modified Patterson map programs to use ascii map files instead of binary map files: utils/PSmap* ============================================================================ Changes for version 1.1 ----------------------- Program: - fixed bug in maximum likelihood targets when using anomalous data - fixed bug in fast translation search that could permit special positions to be searched during molecular replacement - modified DEC Alpha installation to deal with treatment of backslash by the latest Compaq Fortran compiler - modified Linux installations to only use -malign-double flag on x86 based machines - added test in code to try to catch bug in fast math library on some SGIs - added new Makefile options for compilation with fast math library on SGIs - added Makefile for Compaq compilers running under Linux on Alpha platforms HTML Interface: - updated CGI scripts to account for treatment of undef in the latest development version of PERL HTML Documentation: - added flowcharts (in PDF format) for phasing tutorials - added guidelines for MAD and SAD phasing tutorials - added information to the FAQ - possible problems with RedHat 7 on Linux systems - problems with fastmath library under Irix 6.5 on R5000 SGI systems - added recent papers to bibliography Task files: - fixed major bugs in: xtal_refine/composite_omit_map.inp (map was made over most of unit cell instead of around selected atoms) auxiliary/ncs.def (incorrect application of skew matrix) xtal_refine/refine.inp (atom-based parameter corrections were not applied - cis-peptides were not recognized) xtal_util/model_phase.inp (incorrect combination of structure factors from model and bulk solvent) - fixed minor bugs in: general/neighbours.inp (environment option could not be enabled from HTML interface) xtal_phase/mad_phase.inp (f'/f'' values not reported as absolute values in summary file) xtal_mmcif/deposit_mmcif.inp (incorrect binwise free R-values reported) - changes to: xtal_util/analyse.inp (output correlation of anomalous signal between different datasets as both a matrix and by resolution - useful for determining quality of anomalous data for a MAD experiment. Thanks to Tom Terwilliger for suggesting this.) xtal_patterson/patterson_map.inp (set default resolution to be 15A to 4A) predict_patterson.inp ( " ) patterson_refine.inp ( " ) xtal_mmcif/deposit_mmcif.inp (default is to deposit unmodified experimental data, i.e. uncorrected for anisotropy) - new files: general/rms_fit.inp (calculate and apply RMS fit between 2 molecules) Modules: - fixed major bugs in: xtal/scalenbulk (incorrect anisotropic scaling of intensities for the MLI target) - fixed minor bugs in: xtal/twin_operators (incorrect twin operator definition for point group 23) - changes in: xtal/siterefine xtal/printcoordinates (correct printing of f'/f'' values by mad_phase.inp summary file) Libraries: - added toppar/single_atoms.top and toppar/single_atoms.par to provide topology and parameters for isolated carbon and oxygen atoms. These can be used as scatterers when topology information is missing (e.g. when using an EM mask for molecular replacement). Utilities: - none ============================================================================ Changes for version 1.0 ----------------------- Program: - increased field length for reporting cell dimensions read from map and mask files - more informative message when program cannot obtain enough memory - removed use of C preprocessor - faster automatic build of source directory Makefile HTML Interface: - numeric entries can be set to blank to allow cut and paste - error checking for blank numeric entries HTML Documentation: - added entries to FAQ - minor changes to fix typos in tutorials Task files: - fixed major bugs in: xtal_twin/*.inp (incorrect number of reflections selected in some spacegroups) - changes to: general/neighbours.inp (option to write out only residues close to the molecule of interest) xtal_phase/mad_phase.inp (write out f'/f'' values for each scattering type if multiple atom types are used) xtal_refine/bindividual.inp (improved restraint weight estimation) optimize_rweight.inp ( " ) refine.inp ( " ) water_pick.inp (better handling of picking with strict NCS) xtal_twin/bindividual_twin.inp (improved restraint weight estimation) water_pick_twin.inp (better handling of picking with strict NCS) - new files: general/mtf_to_psf.inp (convert MTF file to PSF file) general/molecule_extent.inp (calculate extent of a molecule in orthogonal Angstroms) Libraries: - none Utilities: - fixed bug in mtz_to_cns (writing 2 headers when using CCP4 version 3.5) - fixed bug in to_cns which rejected scalepack reflections when the intensity was equal to -1 ============================================================================ Changes for version 0.9a ------------------------ Program: - revised installation procedure to deal with OSF v3 on older DEC-alpha machines. HTML Interface: - none HTML Documentation: - none Task files: - fixed major bugs in: general/generate_seq.inp (incorrect renumbering of protein residues) xtal_mr/cross_rotation.inp (fastdirect option gives incorrect results) xtal_refine/refine.inp (output coordinate file incorrectly named when user provides an input MTF file) xtal_twin/detect_twinning.inp (crashes if input amplitude data is complex) xtal_twin/detwin_partial.inp (crashes if no input or output test set array is selected) xtal_twin/detwin_perfect.inp (crashes if no input or output test set array is selected) - changes to: xtal_patterson/heavy_search.inp patterson_refine.inp (automatic determination of scattering model for atoms) Libraries: - added missing dihedral parameter (CC-NH1-C-CC) to carbohydrate.param Utilities: - none ============================================================================ Changes for version 0.9 ----------------------- Program: - source code added for ARIA calculations (Michael Nigles, EMBL) - new coordinate minimizer added: Limited-memory Broyden-Fletcher-Goldfarb-Shanno (LBFGS) algorithm, based on the code of Lui and Nocedal (On the limited memory BFGS method for large scale optimization methods. Mathematical Programming 45 1989, 503-528). We are grateful to Greg McMullan (HPCF, University of Cambridge, UK) for providing us with the initial implementation. - fixed bug in xpeakpik.F (out of memory if peaks picked with no atoms present) - new remap function for applying a twinning operator to reciprocal space data - several minor bug fixes - added specific installations for Mac MkLinux and DEC Alpha Linux. Unified installation for other Linux platforms. - installation and execution under both C-shell (csh/tcsh) and Bourne-shell (sh/bash) - modified installation to allow full performance from DEC EV6 - SGI installation can be compiled for larger memory use (>2GB) if required - cns_solve and cns_refine unified into one single distribution HTML Interface: - faster online help - additional CGI scripts for downloading modules, libraries and utilities - PERL version automatically checked - minor changes for formatting HTML Documentation: - tutorial section added (worked examples and other documentation) - frequently-asked-questions list (FAQ) added - bibliography added - links to current libraries, modules and utilities - updated getting started notes (use with different user shells) - updated installation notes (DEC Alpha Linux installation notes) Task files: - fixed major bugs in: auxiliary/ncs.def (calling script terminates if all NCS restraint slots are used in a restraint group) xtal_mmcif/deposit_mmcif.inp (anomalous data treated incorrectly) xtal_mr/cross_rotation.inp (for the realspace rotation search the size of the model P1 box is incorrectly calculated if only a subset of the structure read in is used as the search model) xtal_patterson/patterson_map.inp predict_patterson.inp (3-d Patterson map only covers the asymmetric unit even when the Harker sections are plotted over the extent of the unit cell) xtal_phase/ir_phase.inp mad_phase.inp (script aborts if the derivative name is lower case in the site database file) xtal_refine/model_map.inp (fill-in mode not using calculated data) xtal_refine/water_pick.inp (bulk solvent and anisotropic correction incorrectly recomputed after water addition and peaks on special positions not removed) xtal_refine/fo-fo_map.inp (incorrect map if data incomplete in either dataset) xtal_refine/composite_omit_map.inp model_map.inp ncs_average_map.inp sa_omit_map.inp water_pick.inp (incorrect FOM weighting using the observed map type option) xtal_refine/composite_omit_map.inp ncs_average_map.inp sa_omit_map.inp (inconsistant resolution limits for map and refinement resulted in garbage maps) xtal_util/scale.inp (script terminates when trying to applying Wilson scaling with more than 2000 residues) nmr_calc/anneal_cv.inp ensemble_cv.inp (script aborts if complete cross-validation is turned off without setting all complete cross-validation flags to false) - changes to: general/generate.inp generate_seq.inp generate_easy.inp (simplfied patching of RNA to DNA for DNA structures) general/generate.inp generate_easy.inp (automatic disulphide bond detection for proteins) general/generate.inp generate_easy.inp (automatic chain break detection for proteins) xtal_mr/translation.inp (improved output listing) xtal_mr/translation.inp (translation search peak list can be written for each rotation search tested) xtal_phase/ir_phase.inp mad_phase.inp (option for individual B-factor refinement of grouped atoms) xtal_phase/density_modify.inp (histogram matching option removed, minor changes to calculation of phase differences) xtal_refine/composite_omit_map.inp (can be calculated over a subset of the molecule) xtal_refine/water_pick.inp (new h-bonding criteria for peak deletion, improved defaults) xtal_util/fourier_map.inp (if a model has been read in around which the map will be calculated, picked peaks are mapped as close as possible to the molecule) - new files: auxiliary/refine.def (defaults file for xtal_refine/refine.inp) general/delete_atoms.inp (delete atoms from a structure) general/model_rigid.inp (rigid body minimization of a model) general/psf_to_mtf.inp (convert old PSF format file to new MTF format) general/rename_segid.inp (rename the segment indetifier(s) in a structure) xtal_refine/refine.inp (combined simulated annealing, energy minimization, B-factor refinement, and map calculation) xtal_util/average_friedels.inp (average anomalous information) xtal_util/average_map.inp (apply NCS averaging to an electron density map) xtal_util/flip_friedels.inp (flip anomalous data) xtal_util/mask_map.inp (mask out regions of an electron density map with a mask) xtal_util/model_fcalc.inp (calculate structure factors from a model) xtal_twin/*.inp (task files for refinement of structures with hemihedral twinning) - removed: xtal_phase/ir_refine.inp xtal_phase/mad_refine.inp Libraries: - revised ion.top and ion.param (many more ions, more accurate parameters) - added protein_nohydrogen.top (protein topology with no hydrogens) - added protein_break.top (define patches to remove a peptide link) - added rhombohedral settings for rhombohedral spacegroups (append R to name) - minor bug fixes Utilities: - cns_transfer: transfers CNS parameter information from one task file to another - map_to_omap: convert CNS map to DSN6 format using MAPMAN - mtz_to_cns: convert simple MTZ file to CNS file using mtz2various - fix_dna_rna: reformat PDB nucleic acid file for use in CNS ============================================================================ Changes for version 0.5 ------------------------ Program: - optional use of g77/gcc for compilation on Unix or Windows platforms - fixed bug with BREAK card processing in MTF generation HTML Interface: - none HTML Documentation: - updated installation notes - installation notes for g77/gcc Task files: - modified most map files to perform peak picking and writing of Fourier coefficients. - fixed bug with negative numbers other than -9999 for b_sol and k_sol. - revised and significantly improved density modification protocols Libraries: - added CPR (O name for cis-proline) to protein.top Utilities: - none ============================================================================ Changes for version 0.4a ------------------------ Program: - optimized torsion angle dynamics integration (1.1 to 2 times faster depending on hardware and problem size) - optimized torsion angle dynamics topology generation (2 to 3 times faster) - BREAK card can be used to indicate a chain break for coord/mtf generation - greatly simplified compilation - ported to Windows-NT - stand-alone Windows-NT distribution (self-extracting ZIP archive) - ported to Cray T3E single CPU HTML Interface: - minor bug fixes - minor changes for use with Internet Explorer 4 HTML Documentation: - updated installation notes Task files: - fixed major bugs in: xtal_refine/composite_omit_map.inp xtal_phase/mad_refine.inp xtal_phase/mad_phase.inp xtal_refine/water_pick.inp - changes to: general/neighbours.inp (generate separate PDB file for each neighbour) xtal_refine/composite_omit_map.inp (automatic determination of omit cube size) auxiliary/ncs.def (improved variable names) - new files: general/fractional_transform.inp (apply fractional space transform to mol.) general/realspace_transform.inp (apply realspace transform to mol.) xtal_util/make_hlcoeff.inp (generate HL coefficients from phase and FOM) general/model_anneal.inp (dynamics/annealing without experimental data) xtal_refine/fp_fdp_group.inp (obtain f'/f'' values for anomalous scatters) xtal_refine/water_delete.inp (delete waters from a map based) xtal_refine/fo-fo_map.inp (calculate Fo2-Fo1 map using phases from a model) xtal_util/hlcoeff_blur.inp ("blur" HL coefficients to dampen bias) - renamed: xtal_refine/waterpick.inp to xtal_refine/water_pick.inp - removed: general/transform_molecules.inp - developmental xtal_mmcif/deposit_mmcif.inp (create mmCIF file for deposition of a structure to the structure database) This is currently not accepted at the structure deposition site (PDB), so the pdb submission tool (xtal_pdbsubmission.inp) should be used. Libraries: - none Utilities: - new dos2unix utility for removing ^M characters from a file created on a Windows system. - new isdos utility identifies DOS files (containing ^M) ============================================================================ Changes for version 0.4 ----------------------- Program: - Molecular topology information is stored in a MTF (molecular topology file) format (STAR format). - The internal help facility uses external database files. This help database defines the syntax of the program language for the on-line manual. - ~/ at the beginning of a filename is translated to HOME: HTML interface: - Defaults for input parameters can be passed to the HTML interface. - Online help is available for some input parameters when editing a task file. - The menu of available task files is created dynamically. HTML Documentation: - A HTML based syntax manual is now part of the documentation. - A list of known bugs is provided for previous versions. Task files: - Heavy atom information is no longer stored in the form of a PDB and molecular topology file. These are replaced by a heavy atom site database file. This file contains the appropriate information to describe heavy atoms. The database file has the same format as the header of a CNSsolve task file. The entries are best modified using the CNSsolve HTML task file interface. - A comprehensive set of task files are provided for generation and manipulation of CNSsolve heavy atom database files. Task files are also provided to convert preexisting coordinate and molecular topology files to a CNSsolve heavy atom database format. - New task files are provided for analysis of single models and comparison of two models (see inputs/general). - A simplified generate script (generate_easy.inp) is provided for use with common crystallographic structures (eg. protein/DNA/non-covalent ligands). Coordinate information is provided by the user in one PDB file, disulphide bonds are automatically detected based on distance criteria. - A comprehensive set of NMR structure calculation files are now provided in inputs/nmr_calc. - All known bugs in 0.3c task files have been fixed in 0.4 task files. - Crystallographic task files which output coordinates can output a PDB file which is more O-friendly. If a single character segid is used it will also be written in the chainid column. - For cross-rotation searches a new search option is provided: fastdirect. This option performs a coarse search followed by a fine search around the highest peaks using the direct rotation search. This is significantly faster than a full direct search but in some cases may miss significant peaks. - Task file heavy_search.inp has added site selection criteria based on image-seeking minimum function (IMF) and symmetry minimum function (SMF). - Task file density_modify.inp has the option for gradual phase extension. - Task files density_modify.inp and solvent_mask.inp by default use the local RMS of electron density for solvent mask calculation. Libraries: - Improved parameters for crystallographic refinement of proteins (protein_rep.param). - Harker sections are automatically determined from a library. Utilities: - A new utility, to_cns, for converting both Scalepack/HKL2000 and d*trek reflection files to CNS format is provided. - A new utility, cns_header, is provided for extracting the header information from a task file. - A new utility, cns_info, is provided to print out important information about the program to the screen.