Coot Download Mac Os X

16-04-2021
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4.5 On Mac OSX how do I make the window focus more useful? The default window focusing with the Aqua window manager is a PITA when using Coot. Try typing in a terminal this to set 'Focus Follows Mouse': $ defaults write com.apple.x11 wmffm true. On a more modern version of Mac OS X (10.5+), that might be: $ defaults write org.x.X11 wmffm true. Launch the PHENIX GUI, either by typing 'phenix' at the command line or by launching from your Applications window on Mac OS X. Start a new project with a name such as '1BKRvalidation'. Under the ' Validation ' heading in the right panel of the ' PHENIX home ' window select ' Comprehensive validation '. For Mac: Two options are available: use the Fink package manager, or download a standalone installation. Both are described on Bill Scott's web page. Note that you will need to be running Snow Leopard (OS 10.6) to use many of these, but some obsolete (but still functional) builds of Coot for older OSes are available. The latest gfortran binaries are available from the gfortran wiki, R for Mac OS X' (my preference), HPC on Mac OSX and fink. Note, it is not advisable to use gfortran 4.0 pre 4.0.2 to compile the ccp4 suite. X11: if X is wanted. Install X11.app and the additional X11 SDK from the OS X installation media.

Current Version CCP4 5.0 May 2004

Contents

Requirements
Downloading the Software
Building the Suite on Unix/Linux
Installing Pre-Built CCP4
Installing CCP4 on Microsoft Windows

Appendices:

Also:

Requirements

Compilers
Fortran, C and C++ compilers are needed to build the suite.

Disk Space
To uncompress the standard distribution requires ~235Mbytes(~50Mbytes for the compressed archive file plus ~180Mbytes for theunpacked source code).
Disk requirements for the fully built and installed suite dependson your system and particularly if you use shared libraries. An IRIX6.5system with shared libraries and X-windows software requires ~350Mbytes(after running make and make install),though this can be reduced to around 250Mbytes after installation byperforming make realclean (see 'ReducingDisk Space Requirements for Executables').
The size of the installation may increase significantly if the buildis configured to build any optional packages (see below). For example, building the Clipper and FFTW packages requires ~450Mbytes for installation(which reduces to ~320Mbytes after make realclean).
A minumum cut-down version of the suite (consisting of the compressedtarred files for ccp4-main, lib, include, doc, src and etc) will require~100Mbytes to unpack the distribution.

Some programs use a lot of temporary scratch space to execute - youwill need 10s of MBytes free in the directory pointed at by the environmentvariable $CCP4_SCR, see Scratch Directories.

Other dependencies
The CCP4 graphical user interface CCP4i requires the Tcl/Tk and BLTpackages to be installed on your system before it can be run. (See theseparate CCP4i Installation page)for more details).Optional packages
In addition to the core CCP4 suite and graphical user interface theCCP4 distribution includes a number of optional packages:
Clipper
Kevin Cowtan's C++ libraries for advanced crystallographic functions
FFTW
MIT's fast fourier transform package
10.13By default these packages are not built or installed, and are notcurrently required in order to use the CCP4 suite. To configure installationof the optional packages use the appropriate options in configure (seeConfigure Options).

Downloading the Software

If you are installing on a Unix or Linux system: then decidewhere you want to put the software, for example this might be/usr/local (following usual Unix convention) - this directory islater referred to by the environment variable $CCP4_MASTER.

FTP the compressed tar file ccp4-5.0.tar.gz to thisdirectory (or see Alternative CompressionFormats)

Uncompress the gzipped file :
> gzip -dc ccp4-5.0.tar.gz | tar xvf -

This will create a new ccp4-5.0 directory, in turn containing aboutten new directories(see Directory Structure for details).

Precompiled binaries of the program executables are available for anumber of Unix and Linux-based platforms. If using these precompiled executables it is necessary to download and uncompress the appropriate additional archivefile, see the section on Installing Pre-Built CCP4for further details.

If you are installing under Microsoft Windows: FTP theself-extracting exe file ccp4win5.0.exe and follow the instructions inInstalling CCP4 on Microsoft Windows.

Building the Suite on Unix/Linux

Editing the Setup File

If you have a previously installed CCP4 Suite it is worthwhile lookingat the old $CCP4/include/ccp4.setup as it may save re-editingthe new file (but do a comparison to check there are no new features -Version 5.0 does have some significant changes).The setup file is sourced by users (typically from their .cshrcfile) to create the environment torun CCP4 programs. You will need to customise this file for yoursite.
> cd ccp4-5.0/include
> cp ccp4.setup-dist ccp4.setup(to make two copies of the file -
one is left unchanged for reference).

Edit ccp4.setup following the instructions in the comments - the minimumthat you will need to do is:

  • Set environment variables for CCP4_MASTER (and possibly CCP4)- all other environment variables should follow correctly from theseexcept:
  • Environment variables for the scratch directories CCP4_SCR and BINSORT_SCR(see Scratch Directories).
  • The environment variable CCP4I_TCLTK pointing to thedirectory containing Tcl/Tk executables used by CCP4i (the user interface)- (see the separate CCP4i Installation page).
  • Setup for X-Windows programs which is highly system-dependent(see X-Windows (X11) Graphics Programs for details).
  • Declaring your HTTP_PROXY environment variable (Optional). Otherwise, leave commented out.

    • Source this file - the setting of the environment variables is necessaryfor the rest of the installation:

    > source ccp4.setup

    NB if you are using the bash shell (which is common on someLinux systems) then you will need to create your ccp4.setup file from the$CCP4/include/ccp4.setup-bash file instead (the rest of the instructionsabove still apply).

    If you are unsure whether you are using bash then use the followingcommand:

    > echo $SHELL

    which will return something like /bin/bash.

    Configure and Make

    See Introduction to compilers, configure and makeif you are a novice installer.

    Make sure that you are in the top CCP4 directory and look at a listingof currently supported systems using the configure help option(see ConfigureSystems for more information - essential if you have multiple operatingsystems). Then start the configure process proper:

    > cd $CCP4
    > ./configure help
    > ./configure system options

    where the system is one of those listed by configure help,and must be supplied. There are options for setting non-defaultdirectories, for controlling whether or not certain parts of the Suiteare built, and for overcoming possible problems.The options that you are most likely use are --with-shared-libs and --with-x. See Configure Options for details and a fulllist of options.

    If you are running configure for the first time then before theconfiguration starts a copy of the current CCP4 licensing conditions will bedisplayed and you will be asked whether you agree to them. Foracademic/non-profit users of the software, you should return a completed andsigned copy of the licence, if this has not already been done.

    Copies of the academic licence agreement can be found in various formatsin the $CCP4 directory:

    • academic_software_licence.ps.gz (Postscript file which has been compressed to save space)
    Commercial users of the software should contact CCP4 directly to obtain acommercial licence; see Contacting CCP4. Please note thatall users are required to return a new copy of the licence agreement, even if acopy of the previous license has been already been sent to CCP4.

    To agree to the licence conditions and continue with the configuration, enter'y' at the prompt.

    When the configuration is complete be sure that you are in the $CCP4directory and then run make (to build the executables) and makeinstall to move executables from the src to the bin directory(unless an alternative target directory was specified with the configure--bindir option).

    A reminder for a few people using the configure --bindir option:if you intend to reuse the same executables directory as for a previousCCP4 installation then remove the installed executables with make uninstall.
    > cd $CCP4
    > make(or make > make.log to keep a log file)
    > make install(or make install >> make.log to append to the log file)

    It is generally unnecessary but if you want to test the suite beforeinstallation look at Testing.

    You can save disk space by removing many files which have been movedelsewhere:

    > make realclean

    or, rather than completely deleting files you can leave dummy copiesof the executables so that if the sources get updated, make will only rebuildthe relevant ones:

    > make clean empty-targets

    If you have problems see Problems.

    Install CCP4 Interface

    If you have Tcl/Tk/BLT installed, and have set the environment variables in ccp4.setup correctly, then you should be ready to go. Justtype ccp4i. Information on Tcl/Tk/BLT and on configuringthe interface for local preferences can be found inInstallation of CCP4 Interface.

    Installing Pre-Built CCP4

    Pre-compiled binary versions of the programs are available for someplatforms. It is still necessary to obtain the source code distribution,which contains various data files required by the programs at run-time,and to edit and source the setup file, see above.The set-up script BINARY.setup must also be run to complete theinstallation.

    The procedure for platforms other than Mac OS-X and Microsoft Windowsis as follows:

    1. Download and unpack the main distribution, see'Downloading the Software'
    2. Edit and source the ccp4.setup file, see 'Editing the Setup File'
    3. Download the appropriate binaries for your system and unpack in the top CCP4 directory i.e. $CCP4. This should create the bin subdirectory containing the executables.
    4. Run the BINARY.setup script in $CCP4 to create binary data file and complete the installation.
      NB If you are installing for the first time then you will be asked to agree to the current CCP4 licence before the configuration proceeds.

    The $CEXAM/unix/runnable/run-all script can be run to testthe installation, see Testing the Suite.

    For Mac OS-X the complete binary installation can be performed bydownloading and running the ccp4-5.0_MacOSX.1.dmg.gz, and thenfollowing the steps as per a standard Mac OS-X package installation. ForMicrosoft Windows, see the section onInstalling CCP4 on Microsoft Windows.

    Installing CCP4 on Microsoft Windows

    A version of the CCP4 suite is available which will run under a numberof different Microsoft Windows versions: Windows ME, Windows 95/98,Windows NT V4.0, Windows 2000, and Windows XP. The installation procedureis different from the Unix/Linux platforms but is straightforward:

    1. Make sure you have Administrator privileges (needed to set theappropriate environment variables);
    2. Install Tcl/Tk and BLT (if not already installed);
    3. Download the ccp4win5.0.exe file from the CCP4 ftp server;
    4. Run the ccp4win5.0.exe file to start the installation Wizardand follow the on-screen steps to complete.

    More detailed information is available from theCCP4 on Microsoft Windowswebpage.

    Appendix A - Directory Structure

    The directory structure of the CCP4 distribution under the topccp4-<version-number> directory:
    data
    miscellaneous data required by some of the runnable example scripts
    toxd
    example data and model coordinates for a small protein (alpha-dendrotoxin fromgreen mamba venom: 'toxd')
    rnase
    example data and model coordinates for Ribonuclease fromStreptomyces aureofaciens: 'rnase')
    unix
    runnable
    scripts which can be run with the data in toxd or rnase
    tutorial
    tutorial material for using the CCP4 suite for Data Processing, MIR and MAD phasing, Molecular Replacement and Refinement plus an introduction to the suite and to CCP4i
    ccif
    C library for low level operations on mmCIF files
    clipper
    Kevin Cowtan's Clipper package
    data
    machine-independent `library' files such as the symmetry operators
    fftw
    source code for the MIT `fftw' fast-fourier transform library
    lapack
    src
    source code for the CCP4 library
    man
    Unix manpages for the CCP4 suite
    manual
    LATEX source for the manual and corresponding PostScript file
    src
    program source
    unsupported
    source for the `unsupported' programs
    x-windows
    X-Windows (X11) programs (xloggraph etc.)

    Appendix B: Alternative Compression Formats

    We believe contemporary Unix/Linux systems all supportgzip compression - if yours does not then:

    a) Let us know or we are liable to stop distributing alternatives.
    b) FTP the ccp4-all.tar.Z file and uncompress:

    > zcat ccp4-all.tar.gz | tar xf -

    Appendix C: Introduction to compilers, configureand make

    CCP4 programs are written in either the C, C++ or Fortran programminglanguages (and the source files are called either foo.c, foo.cppor foo.f respectively) and so need either the C compiler (usuallycalled cc), the C++ compiler (which has various names depending on theplatform, for example CC or cxx) or Fortran compiler(usually called f77) to compile and link them. Compilers arereally just programs which process the code to make other programs.'Compiling' is converting the program source code (human readable) intomachine code (computer readable) in an object file called foo.o.

    Large programs are written in several separate source files andso will be made up from several object files. Programs also requiresome standard 'libraries' of commonly used utilities - these are similarto object file and have file names like foo.a. There are some'system' libraries which are a standard part of the operating system ofyour computer and some CCP4 libraries such as mtzlib and symlib which provideutilities to handle MTZ files and symmetry which are used by many programs.The CCP4 libraries also start out as source code in $CCP4/lib/src and needcompiling too. The next stage after compiling is linking (thisis still done by the 'compiler') which is pulling together all the objectfiles and libraries needed for the program to work and creating the 'executable'file (usually just called foo).

    There is an alternative approach to linking programs with the librariesand that is using 'shared libraries'. Linking programs to the defaultarchive library foo.a involves including the necessary library routines in the program executable. Over the suite, therefore, the same code isincluded many times, and a lot of extra disk space is used. In contrast,when a program is linked to a shared library foo.so (createdfrom foo.a by the link editor ld) only a reference tothe library routine is included - it is not actually loaded until runtime.This means that the program executable takes up less disk space, butalso that the program must be able to find the library routine at runtime.For this to work requires that the environmentvariable LD_LIBRARY_PATH is set correctly. This variable is a listof the directories that should be searched to find shared object libraries;it may include the names of several 'system' libraries or libraries fornon-CCP4 programs but should also include $CCP4/lib.

    The process of compiling and linking a complex system such as the CCP4Suite is best done by a utility called make which interprets theinstructions in a makefile. The great usefulness ofmake is that the system 'understands' the dependencies between thevarious levels of the programming system so that, for example, if you changeone file which is used to build many different programs than the make procedure'knows' to recompile and relink all the programs that are affected by thechange. The make procedure will also control other necessaryfunctions such as installing the software (which is basically moving filesfrom where they are first built to where you want them to be used) or anyconfiguring of data or documentation files. It will also clean upby deleting intermediate files.

    It is usual in a complex program system to have several makefiles, onein each directory, always called Makefile. Within CCP4 thereare separate Makefiles in several directories. There is a masterMakefile in the $CCP4 directory which 'calls' all the other makefiles andso to run the make should only require typing the command makein the $CCP4 directory - this command will, by default, use the filecalled Makefile. The make utility can be got to perform some of itsother functions by commands such as make install or make clean.

    There is one more important part of the process, configure.The differences in operating systems and user requirements means it isimpossible to write a makefile which would work for everybody. Theway round this is to edit the makefile before it is run to customise itfor your system. This process is done by a script called configure(which is in $CCP4 directory) which converts a standard initialfile, Makefile.in, into a customised Makefile for your system.The configure process will do a lot of automatic checks on yoursystem (do you have compilers? what system libraries are present?)and has a large number of options for you to set your own requirements.

    So the minimal instructions you will actually need to type for a standardUnix installation are the trilogy:

    > configure
    > make
    > make install

    (but see Building the Suite on Unix/Linux beforetrying it on CCP4!).

    Appendix D: Configure Systems

    When running configure it is necessary to specify the system that you areinstalling on. The following systems are supported:

    irixSGI IRIX operating system (standard 32-bit ABI)
    irix64SGI IRIX operating system (64-bit ABI)
    sunosSolaris SunOS operating system
    sunos64Solaris SunOS operating system, 64-bit version
    aixAIX operating system for IBM
    hpuxHewlett-Packard HP-UX operating system
    osf1DEC/Compaq OSF1 or Tru64 operating system
    linuxLinux operating system with GNU compilers
    linux_compaq_compilersLinux operating system using Compaq compilers
    linux_intel_compilersLinux operating system using Intel compilers
    DarwinMac OS-X operating system
    ia64_linux_eccItanium Linux using Intel compilers
    freebsdFreeBSD operating system for x86 compatible, AMD64, DEC Alpha, IA-64,PC-98 and UltraSPARC® architectures

    If your system does not appear on the list of supported systems forconfigure then use generic.

    Appendix E: Configure Options

    The main configuration parameters (apart from the system type) are controlledby command-line flags to configure of the form

    --<flag>=<value>

    where <flag> may be abbreviated uniquely and = may be replacedby whitespace. The currently-implemented flags of this form are are:

    --srcdir
    The CCP4 source directory (referred to as $CCP4)
    --bindir
    Where the program binaries get installed
    --libdir
    Where the library files get installed

    Other common options are controlled by flags of the form --with-feature:

    --with-shared-libs
    Build shared versions of the libraries libccp4c, libccp4f, libmmdb andlibccif, and link against these (this saves disk space, seeReducing Disk Space Requirements).
    --with-x
    Build theX-Windows-based (X11) programs on some platforms.
    --with-rxdispencer
    Build the distributed version of Henry Spencer's regular expression library (held in $CCP4/lib/rxdispencer). Most unix systems should havetheir own regular expression library, and this option should only be usedif this isn't the case. Currently, the regular expression library is onlyneeded by the CCIF library.

    Other options are:

    --disable-ccif
    Disable installation of the libccif library (held in $CCP4/lib/ccif). This is purely a safety feature in case the new libccif fails on some systems (it shouldn't!). Disabling the ccif library will mean that data harvesting won't work for some programs.One likely cause of failure of the CCIF build is the lack of a localregular expression package, in which case check out the --with-rxdispenceroption first.
    --disable-lapack
    Disable configuration of the LAPACK linear algebra package. By defaultconfigure will search for LAPACK libraries already installed in some formon the system, if none are found then otherwise it will build the netlib`reference' libraries which are distributed with the suite(in $CCP4/lib/lapack).
    To force building of the reference LAPACK libraries regardless of thosealready on the system, use the --with-netlib-lapack option.Disabling the LAPACK is NOT RECOMMENDED as the compilation of a number ofprograms now use the libraries.
    See the MODLIB documentationfor more details about LAPACK.
    --disable-mapslicer
    Disable installation of the MapSlicer Tcl command library. Withoutthis library the MapSlicer viewer will not work.
    --disable-pdb_extract
    Disable installation of the PDB_EXTRACT suite. Certain functionality in the Data Harvesting Manager will not be available.
    --enable-clipper
    Enable configuration and installation of the Clipper package.
    --enable-fftw
    Enable configuaration and installation of the FFTW package included withthe CCP4 suite.
    --with-fftw=dir
    Use an existing FFTW library located in dir, rather thaninstalling the version included with the CCP4 suite.
    --with-warnings
    Include extra compilation flags which output all compiler warnings(normally compilation is silent). This option may be useful for somedevelopers.
    --non_shared
    Don't allow linking against shared libraries (including systemlibraries) when building the program executables. This results insignificantly larger executables but does make them more portable. Notcompatible with --with-shared-libs.
    N.b. This option is only implemented for OSF1 and Linux systems, andcan cause problems if programs are linked against system librarieswhich are only available as shared libraries. Use this optionwith caution.
    --onlylib
    Buildonly the object libraries and not the CCP4 programs (SeeInstalling only the Object Libraries).
    --with-f2c
    Use the free f2c compiler rather than a `native' one.
    N.b. This option is strongly deprecated.

    configure currently assumes that the shareable (plain-text) libraryfiles remain in $CCP4/lib/data rather than being installed elsewhere.

    Coot Download Mac Os X 10.10

    If the build is not done in $CCP4, configure creates src and libdirectories mirroring those in $CCP4 and does the compilations there.

    Configure examines the environment variables necessary for runningthe suite as defined by ccp4.setup and tries to check them as far as reasonable,but these are not actually used in the build process. There are a numberof configuration parameters that you don't usually want to change, butwhose defaults can be over-ridden by the values of environment variableswhen configure is run:

    CC
    the C compiler (default is system's native compiler;another possibility might be gcc )
    COPTIM
    C compiler optimisation flags(default is the highest optimisation which is considered safe or unagressive)
    XCFLAGS
    any extra flags you need to giveto the C compiler, apart from those for optimisation (these are systemdependent)
    CXX
    the C++ compiler (default is system's native compiler;another possibility might be g++ )
    CXXOPTIM
    C++ compiler optimisation flags(default is the highest optimisation which is considered safe or unagressive)
    XCXXFLAGS
    any extra flags you need to giveto the C++ compiler, apart from those for optimisation (these are systemdependent)
    FC
    the Fortran compiler (default is system's native compiler);there isn't currently any support for other than native compilers
    FOPTIM
    Fortran compiler optimisationflags. The default varies, but will have no debugging extras.In some cases (notably IRIX), the default is used because there areso many problems encountered with the optimiser. You may want to tryhigher optimisation levels and see if there's a significant performanceimprovement and that the code still works
    XFFLAGS
    any extra flags necessary forthe Fortran compiler, apart from those for optimisation; you mightwant to change this, for instance to make smaller binariesat the expense of debugging ability
    XLDFLAGS
    any extra flags neededfor ld, typically extra libraries
    RANLIB
    dummy on SysV Unix, ranlibon BSD, depending on whether 'ar -r' builds a symbol tableitself
    LNS
    indicates how to make symbolic links inthe filesystem (usually 'ln -s'), else 'cp' to copy rather thanlink. 'ln' (hard links) could be used in the absence of symbolic linksif you don't need to operate across file systems
    M4
    how to run the m4 macroprocessor and define asymbol to indicate the system type (see configure source)
    MAKE
    the name of the `make' program foruse in recursive Makefiles if the system's make doesn't define the symbolMAKE. Usually null
    SETFLAGS
    set appropriately if individualprograms need special Fortran compiler flags (most likely to suppressoptimisation) - see the configure source
    INSTALL_PROGRAM
    a command to install executables.Uses 'install -c' if a BSD version is available (to avoid interfering with running programs),else 'cp'
    INSTALL_DATA
    a command toinstall non-executables. If BSD install is available,uses 'install -m 644', else 'cp'

    There are corresponding Makefile variables that you can override, e.g.:

    make FOPTIM=-g

    Suppose you support several types of system and share the CCP4 sourceand system-independent data files across a network with a distributed filesystem such as NFS, AFS or RFS. Then it may be convenient to have a subdirectoryin $CCP4 for each system in which to build and, possibly, in which to keepthe resulting binaries. Directories for binaries can be anywhere, though.

    Appendix F: X-windows (X11) Graphics Programs

    The most used X-Windows-based programs are Mosflm (integrate diffractionimages), xplot84driver (used to view map sections and other xplot84 graphicsfiles) and xloggraph (used to view graphs in log files but now superceded byloggraph which is part of ccp4i).The X-windows programs will run on SGIs, DECs and Linux.

    To build X-windows programs you must use the configure --with-xoption and you must ensure that the programs have access tothe resources' relevant application defaults files. This is installationspecific - there is an example for Unix users in ccp4.setup.

    Appendix G: Multiple Installations

    If you wish to do multiple installations for multiple machine types from asingle source code tree, then you should run the script duptree first.This is in the $CCP4 directory and will produce a further script calledduptree_ccp4 containing information on the source directory tree.This second script should then be run once for each machinetype - in each case a duplicate source tree is created with soft linksto the original source. The configure script should then be runwithin each duplicate source tree. The script duptree contains furtherdetails.

    Appendix H: Reducing Disk Space Requirementsfor Executables

    The program executables are big, and you may want to make them smaller.There are various possible ways to do this which are system-dependent:

    Increasing the optimisation level of the compiler might makethe executables bigger or smaller. However, under agressive optimisationthe programs may not work at all. To do this see either ConfigureOptions for ways to change the configuration parameters or use parametersto make , (for example make FOPTIM=-O ).

    Using shared libraries will definitely make executables smaller- use the configure argument --with-shared-libs to build ashared version of the CCP4 library to link against. You must make sureyou have the correct setup, with LD_LIBRARY_PATH defined, to find the sharedCCP4 library at runtime. Beware, using shared libraries has causedproblems in the past when upgrading the operating system or moving executables.
    All systems supporting the dlopen mechanismshould be able to use shared libraries.

    In extremis you can probably save some space by removing all debugginginformation from the executables using the strip programor installing using install -s (see Unix man pagesfor strip or install). This will prevent diagnosing someproblems, though.

    Appendix I: Testing the Suite

    If you want to test the suite before installation then it is necessaryto have the $CCP4/src directory, which currently contains the executables,on the path, for eaxmple, for csh:

    > set path=($CCP4/src:$path)

    You will find two example datasets in $CCP4/examples/toxd and$CCP4/examples/rnase, and some runnable scripts in $CCP4/examples/unix/runnable. Thescript $CCP4/examples/unix/runnable/run-all can also be used toautomatically run the example scripts in sequence and report any failures.

    In addition a set of htmlised CCP4i-based tutorials are available in$CCP4/examples/tutortial. These tutorials cover various aspects ofthe structure determination process using the CCP4 programs, including DataProcessing, MIR and MAD phasing, Molecular Replacement and Refinement.

    Appendix J: Problems Building the Suite

    The amount of testing we can do is limited and there may be installationproblems particularly on less widely-used systems. If you have aproblem..

    First check our problem page (http://www.ccp4.ac.uk/problems.html)

    If there is no reported fix then please try to solve the problem -if you suspect it relates to the library try building the library and runningthe test program for it with make testlibCoot Download Mac Os X. If the problemis in building some of the programs (make

    Cached

    Coot Download Mac Os X fails on the srcdirtarget, having done the libdir target successfully) you can buildas much as possible using:
    > cd $CCP4
    > make -i
    > cd $CCP4/src(or cd $CCP4/unsupported/src)
    > make instsome(This will install the executables which are built and ignore what is missing)

    Finally if you can not solve the problem contact CCP4 (ccp4@ccp4.ac.uk).

    If you find a solution please let CCP4 know; sending patches (made withdiff -c) is very helpful. If you successfully use aconfigure option which reports itself as `untested' or `not properly tested'please let CCP4 know.

    Appendix K: Scratch Directories

    Coot Software Download

    You will need at least 40Mbytes of scratch space to run many of theprograms. The conventional Unix scratch area of /tmp or /usr/tmpis rarely setup with this much space. Many programs run moreefficiently if the space is local to the machine that they are running on.But a potential problem is that if each machine in your laboratory hasits own scratch directory then it is often confusing for users to findfiles on the scratch directory on a remote machine.

    setenv CCP4_SCR /scratch
    setenv BINSORT_SCR /scratch

    Alternatively users can just use the subdirectory in their $HOME areaso:

    setenv CCP4_SCR $HOME/temporary
    setenv BINSORT_SCR $HOME/temporary

    Note that the user interface, CCP4i, also has the idea of a TEMPORARYdirectory which by default is the same as CCP4_SCR but this may need modifyingfor some setups.

    Appendix L: Installing only the Object Libraries

    To build the CCP4 library to support other software systems and avoidthe make procedure attempting to access the src directory,use essentially the same procedure for Building the Suiteon Unix/Linux outlined above, with the following differences:
    1. Use the --onlylib option when running configure, and
    2. Run make onlylib rather than make.

    Appendix M: Installing Updates to IndividualPrograms

    For bug-fix updates distributed as a patch file, you should copy this into$CCP4_MASTER and use the patch program to apply them. There is a short guideto applying patches on the CCP4 web site.

    To rebuild individual programs - put the new source code in $CCP4/src

    > cd $CCP4/src
    > make foo

    Alternatively if you used make empty-targets when you did theoriginal installation then a simple make will just rebuildthe necessary. When you have installed the changes to your satisfactionremove the .orig files left behind by patch.

    > make clean

    Appendix N: Installing Updates to the Whole Suite

    Patch releases of the whole suite may be made from time to time - thesecollect together all bug-fix updates made since the previous release, anddo not introduce any new functionality to the programs.

    Patch releases are made available in a number of ways:

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    1. as complete new source code in a compressed tar file;
    2. as precompiled binaries;
    3. as a source code patch file.

    If downloading the suite for the first time it is best to take the mostrecent available version. Otherwise, the source code patch file can be appliedto a previously installed copy of the suite as follows:

    > cp patchfile $CCP4
    (Move the patch file to the top CCP4 directory)
    > cd $CCP4
    > patch -p1 -N -i patchfile >& patch.log(Apply the patch to the source code using the patch program, and savethe output to a log file)

    If you wish to rebuild any updated libraries and programs then you furtherneed to:

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    > ./config.status
    (Rerun configure with the original settings to regenerate Makefiles)
    > make [install](Rebuild [and install] any updated programs)

    Finally, patch generates files with the extension .orig(one .orig file for each patched file). These files can be removedby running make clean afterwards.

    If using the precompiled binaries you can simply download the latestexecutables as outlined in the section on InstallingPre-Built CCP4. (Please note that it is still a good idea to apply thesource code patch in this case, as this will address bugs in theuncompiled elements of the suite, such as CCP4i and the documentation.)

    Finally, we recommend that you read the notes below before applyingpatches for the first time, and to report any problems with the procedureto CCP4 (ccp4@ccp4.ac.uk).

    Notes on applying patches to the whole suite

    1. Patch files from CCP4 will have names of the formccp4-oldversion-newversion.diff, which indicatesthat the patch will upgrade version old-version to versionnew-version. Applying a patch file to the wrong version will haveunpredictable (and most likely undesirable) results.
    2. It is intended that patches should be incremental, so if youhave e.g. CCP4 4.2 and wish to upgrade to 4.2.2 via the patches,then it will be necessary to first apply the upgrade from 4.2 to 4.2.1,and then that for 4.2.1 to 4.2.2. (It is not necessary to rebuild thesuite inbetween applying the patches however.)
    3. The patch files cannot upgrade binary files (such as MTZ data files,images, and precompiled Java files) which are included in thedistribution.
    4. It is sensible to keep a log file from the patching procedure (seeinstructions above), in case the patching is unsuccessful. In the eventof a problem, please send the details along with the log file toccp4@ccp4.ac.uk.
    5. To reverse the patch follow the instructions above, including anadditional -R option on the patch command.

    Appendix O: Uninstalling the Suite

    If it is necessary or desirable to undo the installation and start againfrom scratch (for example you wish to run the configuration with differentoptions) then the following prescription should restore the originaldistribution:
    > cd $CCP4
    > make uninstall(Delete all the installed files, e.g. libraries in $CCP4_LIB and binaries in $CBIN)
    > make distclean(Delete all the files created in configuring and building the suite, including the Makefiles)

    It will then be necessary to re-run configure etc as if starting from scratch.This procedure should also work for individual sections of the suite, forexample if you want to uninstall and remake the libraries then cd $CLIBSinstead before executing make uninstall and make distclean.

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    Appendix P: Contacting CCP4

    Completed licence agreements and requests for commercial softwarelicences should be mailed or faxed to:

    The Secretary to CCP4
    Daresbury Laboratory
    Warrington WA4 4AD
    UK

    		Telephone: (+44) 1925 603929 (direct line)
    Facsimile: (+44) 1925 603825
    e-mail: ccp4@ccp4.ac.uk

    Technical queries including reports of problems with downloading,installing or running the software should in the first instance besent to us by e-mail at ccp4@ccp4.ac.uk.