CCP4 v6.0 Program Changes

INDEX

Building etc
Program changes
Library
New programs
Graphical User Interface
Documentation
Withdrawal
Examples

A list of general acknowledgements for testing CCP4 v6.0 can be found here.

• Clipper/fftw built by default
• cctbx/phaser are included as separate packages. The main CCP4 build will build them if these packages are included.
• There are a number of fixes for the AIX build.
• to_small_refmac.csh/to_big_refmac.csh: shell scripts to reduce and restore the array sizes for Refmac5 prior to compilation (in $CPROG/refmac5_/)
• A new ccp4.setup-zsh for ZSH users (Bill Scott)
• --with-x is now the {default;} use --disable-x if you have problems with the X-windows build
• The script patch_ccp4.sh in {$CETC} can be used to automatically download and apply available source code fixes to the suite for UNIX-based systems. Note that any recompilation must still be performed manually afterwards - see Appendix M of the CCP4 installation instructions.

• ANISOANL: now checks for non-positive-definite Us in XYZIN and lists to log file (all options)
• AREAIMOL: new REPORT keyword allows control of output for contact areas and reporting of area by residue
• CIF2MTZ: several new column labels added, including anomalous
• COORD_FORMAT: new keyword FIXBLANK
• DM: program now produces a data harvesting file
• MapSlicer: supports reading and display of mask files (new "mask" mode); displays "greyscale" view superimposed on contours; saves user preferences for contour levels and other settings between sessions.
• MTZ2VARIOUS: if F(+) and F(-) are input for SHELX output then rescaling is done within the program to produce pseudo-intensities; OUTPUT CIF option updated to use tokens from the PDB exchange dictionary for anomalous data and HL coefficients.
• PDBCUR: new keywords SUMMARISE, DELHYDROGEN, MOSTPROB, CUTOCC, and TRANSLATE (MDW)
• PDB_EXTRACT: new version 1.700
• PDBSET: new function ATRENUMBER (renumber atoms sequentially without gaps in output file)
• PEAKMAX: new keyword EXCLUDE (turns suppression of peaks at the edge of the map on or off)
• REFMAC: new version 5.2.0019
• MOLREP: new version 9.0.09
• MOSFLM: new version 6.2.5
• SFCHECK: new version 7.0.18
• SFTOOLS: new options LIST/SET DCELL/DWAVE for dataset information
• Matthews_coeff: outputs the Kantardjieff and Rupp resolution based probabilities
• FFTBIG replaces FFT
• SCALEPACK2MTZ SYMM keyword not compulsory anymore, will try to pick up spacegroup in the input file.
• TLSANL: ANISOU line in XYZOUT is now adjusted according to ISOOUT keyword. Summary tags used to highlight important quantities.

• CCPERR/ccperror: each time ccperror is called it invokes a user-defined callback function which has previously been set using new C library function "ccp4SetCallback".
• CCTBX library included as a separate package (Paul Adams, Ralf Grosse-Kunstleve et al)

• BP3: multivariate likelihood substructure refinement and phasing of S/MIR(AS) and/or S/MAD (Raj Pannu)
• CHAINSAW: new molecular replacement utility that mutates a pdb file to poly-serine using a sequence alignment (Norman Stein)
• PDB_MERGE: jiffy to merge two PDB files (Martyn Winn)
• PHASER 1.3: molecular replacement (Randy Read et al)
• PIRATE (cpirate): statistical phase improvement (Kevin Cowtan)
• SUPERPOSE: secondary structure alignment (Eugene Krissinel)

• Version 1.4.4
• AREAIMOL: new option to generate pairwise area differences for "molecules" (defined as arbitrary groups of chains) in a PDB file.
• CRANK: interface to automated structure solution via experimental phasing (currently SAD, SIR and SIRAS data)
• SHELX C/D/E: interface to running the SHELX C, D and E programs standalone or as a pipeline in order to perform heavy atom search and phasing
• CHAINSAW: interface to new program of the same {name;} mutates a pdb file to poly-serine using a sequence alignment for molecular replacement
• Scale and Merge Intensities (SCALA): option to output Scalepack formatted reflection files suitable for input into SHELX or SOLVE (corresponds to OUTPUT POLISH UNMERGED option of SCALA)
• Run Remote Jobs: option to use either rsh or ssh to run jobs on remote machines.
• Output in different map formats: the interface should now only offer output in the formats (O, QUANTA) that can actually be created with the user's setup
• CreateLabinLine4: extended version of CreateLabinLine that allows groups of up to four related labels to be specified, for example H-L coefficients or F(+)/sigF(+) and F(-)/sigF(-) groups. This command also supports a -command option similar to other CreateLine-type commands. See the documentation for details.
• FindExecutable: new command, return full path of a program executable
• Install Task: export task now allows save/restore of {parameters;} tasks can be defined as basename/directory pairs; version number included in archive filename.
• Logfile viewer: when viewing a long file, there is now the option to look at the previous frame as well as the next one.
• MTZ handling: new commands GroupMtzCols, MtzColSameDataset, GetMtzColType, GetMtzGroupByType.
• WarningMessage: has new options -image, -font and -color
• Superpose: when fitting atoms from one PDB file to another, atom numbers given by the user now refer to those specified in the file (rather than to the positions in the file)
• types.def: added new types _res_file (ShelxD result file) and "_phs_file" (XtalView phases file)
• File Selection for Windows: drive can also be chosen from the file browser.
• Disabled tasks: some task interfaces will be unavailable to users if "prerequisites" (as defined in the taskname_prereq procedure in the task interface file) are not found on the user's system. "Disabled" means that the task button will be non-functional and the text will be greyed-out. Check the documentation $CCP4I_HELP/general/additional.html for information on how to enable these tasks.
• Project Switching: Having a small menu button enabling to instantly switch between projects without passing through "directories" interface
• Database search/sort: Having a new Button search/sort popping up a window enabling users to do various kinds of simple/advanced search and/or sorting also be able to refine sorts or searches.
• CreateToggleFrame: new option -justify allows programmer to specify the positioning of the subframes (left, right or center).

• Added documentation on adding doc comments for CCP4i core commands ($CCP4I_HELP/progdocs/documenting.html)
• alternate_origins.html: updated with spacegroup numbers, information about alternative settings and Hermann-Mauguin symbols
• Loggraphs: documentation for TABLE, GRAPHS, SCATTER etc now in loggraphformat.html (see "File Formats" section)

• fft (replaced by fftbig )

• abs, bp3, chainsaw, pdb_merge, phaser, pirate, superpose examples added
• New examples for using python interface to cctbx and phaser (cctbx_py_test.exam and phaser_py_test.exam)