NAOMI Command Reference NAOMI Quick Command Reference
NAOMI

If you can't quite remember the exact syntax of a command that you want to use, here's an alphabetically ordered list with links to documentation.

Watch out for the underscore characeters in some commands - these don't show up too well in the links!

analyse complex hbonds

analyse complex hydrophobic

analyse complex salt-bridges

analyse ensemble

bad contacts

calc (phi, psi, chi etc...)

characterise hbond sites

characterise electrostatic sites

characterise hydrophobic sites

correct

displacement B-factors

displacement rmsds

disulphide placement analysis

engineer disulphides

for pdb list

idcodes on/off

insight on/off

make side-chain ensemble-1

minimize bad contacts

molscript contacts

molscript hbonds

molscript on/off

molscript sec_struc

molscript sec_struc_col1

molscript sec_struc_col2

mutate

pack structures

pdbtolib

pdb_write

predict folding intermediate

predict possible binding sites

predict protein-protein interactions

predict noes

protwrite

ramabox

ramachandran

ramaconcat

ramaend

randomize (generating families of random 
                        structures)

random ssed

read pdb

repair side-chains

reset resnum

residue library size

residue limit

select

set pdb dir

set report dir

set torsion

side-dev_axes

plot_side-dev

side-dev_end

system

table chain-breaks

table conect_records

table exterior_residues

table hairpins

table hbonds_ad

table hbonds_da

table hbonds_dump

table hbonds_sidedump

table hydrophobic

table interior_residues

table key_residues

table posphi

table proconf

table protein

table residue_access

table resol

table salt-bridges

table sec_struc

table side-chain_hbonds

table structre_info

table total_access

terminii X-PLOR

use chain-breaks

use covalent_bonds

use disulphides

use hairpins

use hbonds

use sec_struc

use solvent access

validate

write

zone