Xplor-NIH on Biowulf
XPLOR-NIH is a structure determination program which incorporates the legacy X-PLOR program, but utilizes a Python interface and includes facitiles for structure determination using observables from NMR, EPR, Cryo-EM, SAXS and other experiments.
Xplor-NIH is developed in the Computational Biomolecular Magnetic Resonance Core within the NIDDK Laboratory of Chemical Physics.
Documentation
Important Notes
- Module Name: Xplor-NIH (see the modules page for more information)
- Additional environment variables set: XPLOR_NIH_TOPPAR = location of topology/parameter files for that version
- Xplor-NIH requires the usual set of Xplor input files -- coordinates, xplor input files, topology/parameter files. The 'standard' files are in $XPLOR_NIH_TOPPAR, the envronment variable that is set when the module is loaded.
- To run a job on Biowulf, please use the slurmXplor helper.
- Sometimes a large Xplor-NIH slurm job will hang at startup time. In this case, try adding the option -startup_delay 1 to the command-line.
Batch job
Most jobs should be run as batch jobs.
[user@biowulf ~]$ slurmXplor -py -ntasks num -partition partitionName [options] script.py
where num is the number of processes to run and options are any option to the xplor command. It is also possible to specify arbitrary sbatch options. For details please see
[user@biowulf ~]$ slurmXplor -help