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XCrySDen
Overview
XCrySDen (X-Window CRYstalline Structures and DENsities) is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.
Version 1.5.60 is installed on the CSF.
Restrictions on use
There are no restrictions on accessing this software. It is made available under the GNU GPL v2 license.
The software can be run with the ability to call Crystal. To do so, you must be in the crystal group on the CSF, which requires that your research group has a Crystal license. See below for more information on running the software with and without Crystal support.
Set up procedure
To access the software you must first load the modulefile:
module load apps/gcc/xcrysden/1.5.60
If you are in the crystal unix group and wish to run with Crystal support enabled, you should also load the Crystal modulefile:
module load apps/intel-12.0/crystal/c09_201_emt64
One-time Setup
Before running xcrysden for the first time you should copy a config file to your home directory. Please do one of the following on the CSF login node:
- If NOT using crystal with xcrysden
mkdir ~/.xcrysden cp $XCRYSDEN_HOME/custom-definitions ~/.xcrysden
- If using crystal with xcrysden
mkdir ~/.xcrysden cp $XCRYSDEN_HOME/custom-definitions.with-crystal ~/.xcrysden/custom-definitions
Running the application
Ensure you have done the one-time setup above.
Please do not run xcrysden on the login node. Jobs should be run interactively on a compute node using the qrsh command. You must have logged in to the CSF with X11 forwarding enabled. Please see the interactive guide for more details.
Interactive usage
Start an interactive session from the login node:
qrsh -l inter -l short
Wait until you are logged in to a backend compute node, then:
module load apps/gcc/xcrysden/1.5.60 # Optional if using crystal module load apps/intel-12.0/crystal/c09_201_emt64 # Start xcrysden xcrysden
X11 Errors
If you receive errors about X11, for example:
X Error of failed request: BadValue
then please try setting the following environment variable just before running xcrysden:
export LIBGL_ALWAYS_INDIRECT=1
Further info
Updates
None.