This requires a build of Coot that includes a working Pythoninterpreter; if the PHENIX extensions are not functioning, this is almostcertainly due to the lack of Python in the Coot build. A few specific paths are searchedautomatically. On Mac, most installations should be automatically detected,but you may need to set the path explicitly to ensure that the correct versionis used. We distribute anobsolete binary build of PyMOL version 0.
A variety of options are available for both Linux and Mac, includinginstallation via some package managers Fink, and some Linux distributions ,custom installation from source, or proprietary builds with additionalfeatures purchased from Schrodinger. Additional support is available. For older versions of Mac OS A few specific paths are searched automatically.
On Mac, most installations should be automatically detected, but you may need to set the path explicitly to ensure that the correct version is used. We distribute an obsolete binary build of PyMOL version 0.
Configure and Make See Introduction to compilers, configure and make if you are a novice installer. Make sure that you are in the top CCP4 directory and look at a listing of currently supported systems using the configure help option see Configure Systems for more information - essential if you have multiple operating systems.
There are options for setting non-default directories, for controlling whether or not certain parts of the Suite are 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 full list of options. If you are running configure for the first time then before the configuration starts a copy of the current CCP4 licensing conditions will be displayed and you will be asked whether you agree to them.
Please note that all users are required to return a new copy of the licence agreement, even if a copy of the previous license has been already been sent to CCP4.
A reminder for a few people using the configure --bindir option: if you intend to reuse the same executables directory as for a previous CCP4 installation then remove the installed executables with make uninstall. Just type ccp4i. 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.
For Mac OS-X the complete binary installation can be performed by downloading and running the ccp Compilers are really just programs which process the code to make other programs. Large programs are written in several separate source files and so will be made up from several object files. Programs also require some standard 'libraries' of commonly used utilities - these are similar to object file and have file names like foo.
There are some 'system' libraries which are a standard part of the operating system of your computer and some CCP4 libraries such as mtzlib and symlib which provide utilities to handle MTZ files and symmetry which are used by many programs. The next stage after compiling is linking this is still done by the 'compiler' which is pulling together all the object files 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 libraries and that is using 'shared libraries'. Linking programs to the default archive library foo. Over the suite, therefore, the same code is included many times, and a lot of extra disk space is used. In contrast, when a program is linked to a shared library foo. This means that the program executable takes up less disk space, but also that the program must be able to find the library routine at runtime.
The process of compiling and linking a complex system such as the CCP4 Suite is best done by a utility called make which interprets the instructions in a makefile. The great usefulness of make is that the system 'understands' the dependencies between the various levels of the programming system so that, for example, if you change one 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 the change.
The make procedure will also control other necessary functions such as installing the software which is basically moving files from where they are first built to where you want them to be used or any configuring of data or documentation files. It will also clean up by deleting intermediate files. It is usual in a complex program system to have several makefiles, one in each directory, always called Makefile. Within CCP4 there are separate Makefiles in several directories.
The make utility can be got to perform some of its other 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 is impossible to write a makefile which would work for everybody. The way round this is to edit the makefile before it is run to customise it for your system. The configure process will do a lot of automatic checks on your system do you have compilers?
Appendix D: Configure Systems When running configure it is necessary to specify the system that you are installing on. The following systems are supported:. If your system does not appear on the list of supported systems for configure then use generic.
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