wARP logo Software for Macromolecular Crystallography
ARP/wARP Copyright 2016
by European Molecular Biology Laboratory



Frequently Asked Questions


Installation: How to install ARP/wARP 7.6?

Distribution

The 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 Installation

Unless 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.
  1. Download arpwarp_7.6.dmg from the either ARP/wARP or CCP4 website.
  2. Double click on the downloaded file.
  3. Double click on the ARPwARP installer.
  4. Agree to the ARP/wARP license.
  5. Select a destination drive.
  6. Choose destination directory if the default /Applications is not suitable.
There should not be problems with the installation. However, if there are any, we encourage you to save the installation log that is displayed and send it to the ARP/wARP developers using the link on the ARP/wARP homepage.

Standalone Command Line Installation on Mac OSX or Linux

Unless 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.

  1. Download the full ARP/wARP package arp_warp_7.6.tar.gz from the ARP/wARP or CCP4 web site and save it in a location of your choice. Next, type:

  2. % gunzip arp_warp_7.6.tar.gz
    % tar xvf arp_warp_7.6.tar


    The 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.

  3. Go to the directory arp_warp_7.6 and run there the install.sh script by simply typing

  4. % ./install.sh

Unless you are already an experienced ARP/wARP user, you should try to get started with the test files provided in the directory arp_warp_7.6/examples. These include data for protein chain tracing (also with NCS), helix/strands search, nucleotides, ligand and solvent building. README files are included which give more detailed information regarding which data are to be used for what purposes.

If things do not work as expected please consult your more experienced colleagues, system manager or the ARP/wARP developers.

Installing for Multiple users

The 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.sh

At 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-csh


where 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.csh

where /destination-arpwarp is the location where ARP/wARP was installed.

Installation of ARP/wARP-CCP4 as a bundle

ARP/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 patch

If 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.tgz

To 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: What is new in ARP/wARP 7.6 ?

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.
Specifically:

Protein model building

  1. Dipeptide conformational space is introduced for the selection of the chain path
  2. NCS restraints are now default at resolution 1.5 A or lower
  3. Side chain fit is improved with additional real-space refinement
  4. Check for java is introduced and the use of conditional restraints is turned off if java is not installed (can occur on OSX 10.10 and 10.11).

DNA/RNA building

  1. The tracing of the nucleotide chain tracing is enhanced with the addition of the second algorithm for phosphate detection
  2. Chain tracing now proceeds in 5-cycle iterative manner, as for the protein chain tracing

Solvent building

  1. Default density thresholds for atom update are optimised

Other changes

  1. ARP/wARP installer is made more robust

TCL: The installer reports a problem with the TCL version. What can I do ?

Problems with TCL

There 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.

A Solution

  1. Download TCL version 8.4 for the Mac or Linux from Active State. Active State provide a free and easy to use TCL installer.
  2. Install TCL by double clicking on the DMG (Mac) or using install.sh (Linux).
  3. Go to the install directory of the failed ARP/wARP installation (e.g /Applications/arpwarp_7.6 on Mac OSX).
  4. Edit install_csh.sh and change the 4 occurrences of the string:
    $CCP4I_TCLTK/tclsh
    to the path of the new tclsh that you have installed. On Mac OSX this is:
    /System/Library/Frameworks/Tcl.framework/Versions/8.4/tclsh8.4
  5. Run the following command from a terminal in the ARP/wARP installation directory:
    sudo ./install.sh
The ARP/wARP installation should complete without problem.

Fink CCP4: A REFMAC error is reported when running with Fink version of CCP4

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:
REFMAC5

used 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.
  1. The recommended workaround is to install CCP4 7.0.
  2. A quick workaround is to turn off conditional restraints.
  3. It is also possible to prevent this problem by compiling Refmac with gfortran version 4.4.

Kernel too old: FATAL: kernel too old

The following error appears, during installation, on some older version of Linux:

FATAL: kernel too old
Segmentation fault


This 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.