Submitted by snerli on Wed, 05/24/2017 - 21:04
Description:
Nmr Exchange Format (NEF) is a fairly inclusive file with chemical shift list, unassigned noesy peak lists, noe restraint list, rdc list and linkage table. NEF spec can be found here.
Usage:
| nef.py |
[-h] [-method {autoNOE,rasrec}] [-fasta FASTA] |
| |
[-seq SEQ] [-prot PROT] [-cs CS] [-restraint RESTRAINT] |
| |
[-rdc RDC] [-peaks [PEAKS, [PEAKS ...]]] [-NEF NEF] |
Detailed Help:
| -h, --help |
show help message and exit |
| -method {autoNOE,rasrec} |
method used to perform structure calculation |
| -fasta FASTA |
FASTA file of the protein |
| -seq SEQ |
.seq Format file |
| -prot PROT |
provide .prot chemical shift file (use with -method autoNOE) |
| -cs CS |
provide .tab chemical shift file (use with -method rasrec) |
| -restraint RESTRAINT |
provide .cst restraint file |
| -rdc RDC |
provide rdc restraint file if available |
| -peaks [PEAKS, [PEAKS ...]] |
provide noesy peaks separated by a space |
| -NEF NEF |
provide name for output NEF file |
Examples:
nef.py -fasta nEIt.fasta -prot nEIt_curated_renum.prot -cs nEIt_curated_renum.tab -restraint noe_auto_assign.cst -rdc nEIt.rdc -peaks HCCH.clean.peaks HCNH.clean.peaks -NEF CSROSETTA_test1.nef