CYANA
Software description
CYANA (© by Peter Güntert) is a program for automated structure calculation of biological macromolecules on the basis of conformational constraints from NMR. The combination of automated NOESY cross peak assignment, structure calculation with a fast torsion angle dynamics algorithm, and the ease-of-use of CYANA provide for unprecedented efficiency in NMR protein structure determination.
License
NSC has a site license that allows academic users in Sweden to run Cyana without restriction on NSC systems, given that they conform to the Cyana academic license for computer centres. Please contact NSC support if you are interested in using Cyana at NSC. We will then share a copy of the license agreement and ask you to acknowledge that you have read and accepted the Cyana license terms.
Job script example
#!/bin/bash
#SBATCH --time=120
#SBATCH --nodes=1
#SBATCH --ntasks=9
#SBATCH --account=snic202X-Y-ZZ
module load CYANA/3.98.15-bdist-compat-el7
# Remember to edit the name of the input file for a new job
inputfile=CALC.cya
outputfile=${inputfile%.cya}.out
# Echo a few things to the output file
date +'%d-%b-%Y %H:%M:%S' >> $outputfile 2>&1
t0=`date +%s`
cyana -x -t intel-openmpi -c 'mpprun --compat el7' >> $outputfile 2>&1
echo "nproc=$(($SLURM_NTASKS - 1))" >> $outputfile 2>&1
# Start the job
cyana -t intel-openmpi -c 'mpprun --compat el7' << EOF >> $outputfile 2>&1
erract:=abort
nproc=$(($SLURM_NTASKS - 1))
${inputfile%.cya}
quit
EOF
echo >> $outputfile 2>&1
t1=`date +%s`; t1=`expr $t1 - $t0`
echo "Total elapsed time: $t1 s" >> $outputfile 2>&1
date +'%d-%b-%Y %H:%M:%S' >> $outputfile 2>&1
Command line example
The easiest way to submit a Cyana job is to use the cyana script:
module load CYANA/3.98.15-bdist-compat-el7
cyana -n 8 CALC.cya
Homepage: www.las.jp/english/products/cyana.html
Available Modules
3.98.15-bdist-compat-el7
Note: This module uses an EL7 compatibility container.
Installation of CYANA version 3.98.15.
Load with:
[user@system ~]$ module load CYANA/3.98.15-bdist-compat-el7
Installed documentation
/software/sse/manual/CYANA/3.98.15/bdist/help/cyana
Online documentation
http://www.cyana.org/wiki/index.php/CYANA_3.0_Reference_Manual