Software for Macromolecular Crystallography
ARP/wARP Copyright 2016
by European Molecular Biology Laboratory
DistributionThe recommended way to obtain and install ARP/wARP is through a download and install of a joint CCP4 7.0 - ARP/wARP 7.6 bundle (available from http://www.ccp4.ac.uk/). The users can also obtain and install a standalone version of ARP/wARP, either from http://www.arp-warp.org/ or from the CCP4 download site at http://www.ccp4.ac.uk/. When using a standalone version of ARP/wARP, CCP4 7.0 is the lowest recommended version to use with ARP/wARP 7.6. Older versions of CCP4 will probably work but they have not been tested with the latest ARP/wARP 7.6 features.
Standalone Intel Mac OSX InstallationUnless installing a joint CCP4 - ARP/wARP bundle, CCP4 must be installed before ARP/wARP installation is attempted. Sudo permissions may be required. There could be problems installing ARP/wARP when CCP4 is installed using 64-bit Fink.
Standalone Command Line Installation on Mac OSX or LinuxUnless installing a joint CCP4 - ARP/wARP bundle, CCP4 must be installed before ARP/wARP installation is attempted. There could be problems installing ARP/wARP on Mac OSX when CCP4 is installed using 64-bit Fink.
% gunzip arp_warp_7.6.tar.gz % tar xvf arp_warp_7.6.tarThe package will unpack under the directory called arp_warp_7.6 that will contain all the required files and subdirectories. The installation script install.sh is needed to do the installation and to set the appropriate environmental variables. Sudo permissions may be required. The `README` will walk you through the installation process.
Installing for Multiple usersThe recommended way to install ARP/wARP, so that it can be shared by multiple users, is by doing a command line install. The user who is doing the installation should have both write permission to the installation directory and write permission to the CCP4 installation directory.
% gunzip arp_warp_7.6.tar.gz % tar xvf arp_warp_7.6.tar % cd arp_warp_7.6 % ./install.shAt the end of the installation, the CCP4 startup files will be updated with an addition similar to following lines: (for c-shell)
## Line below added by ARP/wARP 7.6 installer test -r /destination-ccp4/bin/arpwarp.source-csh && source /destination-ccp4/bin/arpwarp.source-cshwhere destination-ccp4 is the $CCP4 directory. The file /destination-ccp4/bin/arpwarp.source-csh will be created and will contain the following instruction
test -r /destination-arpwarp/arpwarp_setup.csh && source /destination-arpwarp/arpwarp_setup.cshwhere /destination-arpwarp is the location where ARP/wARP was installed.
Installation of ARP/wARP-CCP4 as a bundleARP/wARP can be installed together with CCP4 by downloading the joint bundle, directly from the CCP4 web site. Both packages can be obtained and installed with a single mouse click.
Installation of the patchIf you have already downloaded earlier ARP/wARP version 7.6 without a patch, you can download and install the patch only:
arp_warp_7.6_patchXX_only.tgzTo install it, make sure your ARP/wARP 7.6 is active. Then type:
tar -xzvf arp_warp_7.6_patchXX_only.tgz -C $warpbin/../../../You may need to use 'sudo' priviliges to untar the patch.
Major changes in Version 7.6
ARP/wARP 7.6 provides improved performance in protein chain tracing, particularly at resolution below 2.5 A, as well as in DNA/RNA fragment building.
Protein model building
Problems with TCLThere is a bug in TCL 8.5 that prevents third party software, such as ARP/wARP, from installing into the CCP4 interface. This bug only affects installation, once ARP/wARP is installed it is unaffected by the version of TCL. Should you experience with this bug, you can install ARP/wARP using the instructions below.
$CCP4I_TCLTK/tclshto the path of the new tclsh that you have installed. On Mac OSX this is:
The following error:
### CCP4 X.X: Refmac_X.X.XXX version X.X.XXXX : XX/XX/XX ## QUITTING ... ARP/wARP module stopped with an error message: REFMAC5used to sometimes occur earlier in ARP/wARP classic model building jobs when used with previous versions of Refmac that have been compiled with gcc/gfortran 4.6.0 and above. There are two main workarounds at the moment.
The following error appears, during installation, on some older version of Linux:
FATAL: kernel too old Segmentation faultThis then leads to a, possibly false, warning about the hardware lacking the SSE2 instruction set. The issue is actually caused by the Kernel on the machine being too old to support some of the libraries that are statically linked into ARP/wARP. We are investigating to see if there is a straightforward solution to this problem. However, if it is at all possible, we recommend upgrading the version of Linux on the machine that reports this error since older versions of Linux may experience further problems with ArpNavigator 3D graphics support.