Protein Features Documentation

Using LOMETS

The LOMETS runscript is in the I-TASSER suite code, specifically at /n/groups/drad/I-TASSER4.3/I-TASSERmod/runLOMETS.pl.

To run, LOMETS just requires a path to the I-TASSER package, some library files, java, and the directory where it can find a .fasta file containing your sequence of interest.

Specifically, I use these arguments:

  • -pkgdir: Path to the main I-TASSER directory. So, /n/groups/drad/I-TASSER4.3/.
  • -libdir: Path to library packages for I-TASSER. So, /n/groups/drad/I-TASSER4.3/ITLIB.
  • -seqname: The sequence name (I use uniprot id) for the sequence you're modelling. For example, Q9Y5Z9.
  • -java_home: Path to a java distribution. We use /n/app/java/jdk-1.8u112.
  • -runstyle: See the I-TASSER docs for more info. We use serial.
  • -homoflag: See the I-TASSER docs for more info. We use real.
  • -outdir: Where will LOMETS put intermediate and output files? I usually just use the same directory where I put the .fasta file.
  • -usrname: Your O2 username. For example, Roger's is rlc18.

Here's an example full O2 script:

#!/bin/bash
#SBATCH -J LOMETS_O75446
#SBATCH -p short
#SBATCH -t 00-06:00
#SBATCH --mem 1500M
#SBATCH -o /home/js741/CarbonylationSite_Prediction/Human_Proteins/lomets_helpers/LOMETS/main/O75446/logs/lomets_run.out
#SBATCH -e /home/js741/CarbonylationSite_Prediction/Human_Proteins/lomets_helpers/LOMETS/main/O75446/logs/lomets_run.err
/n/groups/drad/I-TASSER4.3/I-TASSERmod/runLOMETS.pl -pkgdir /n/groups/drad/I-TASSER4.3/ -libdir /n/groups/drad/I-TASSER4.3/ITLIB/ -seqname O75446 -datadir /home/js741/CarbonylationSite_Prediction/Human_Proteins/lomets_helpers/LOMETS/main/O75446 -java_home /n/app/java/jdk-1.8u112 -runstyle serial -homoflag real -outdir /home/js741/CarbonylationSite_Prediction/Human_Proteins/lomets_helpers/LOMETS/main/O75446 -usrname js741
← LOMETS OverviewMetal Binding Overview →