ARIA

YES

Two versions are working and MUST be run using SGE.

Aria 1.1 and Aria 1.2 have been tested and work.

see here for in-house conversion scripts for Aria1.1 and Aria1.2.

MUST be run on cluster via SGE. Do not use more than 10 processors

How much faster is using ARIA on SGE?

for Aria1.1 setup

Aria1.2: setup

For running on multiple machines

RUN USING SGE

XPLOR-NIH

YES

NIH version of xplor. Must use SGE to run..

MUST be run on cluster via SGE.

How much faster is using Xplor on SGE?

USE SGE TO RUN

CNS

YES

The CNS suite for calculating structures. Must run via SGE.

How much faster is using CNS on SGE?

USE SGE TO RUN

CYANA

YES

Only non-parallel version working at moment, but you can use two processors by introducing the command nproc=2 in you CALC.cya file

/nfs/home/osborne/local/cyana-2.1/cyana

HADDOCK

YES

Calculates structures of complexes based on limited restraints. Can be run on cluster via SGE

How much faster is HADDOCK using SGE?

Check with mike how to run this

See here for Haddock setup, or source the following file:

/nfs/home/osbornem/local/haddock1.3/haddock_configure

and type haddock1.3

USE SGE TO RUN

Molmol

YES

From Wuthrich's lab. Has some nice interactions with NMR data in CYANA format. Can get great pics, using Povray

molmol

Pymol

YES

A great package for generating pictures (via Povray) or movies.

I have also installed numerous plugins, e.g. for electrostatic calculations (apbs) and movies (pymike)

Some example movies: mpeg mpeg1 and a high res avi

pymol.com

pymike

vmd-xplor

YES

Visualiser, really nice for analysis of output from CNS/XPLOR

vmd-xplor

Grasp

YES

WILL ONLY RUN ON THE SGI's, nice for electrostatics

grasp

Chimera

YES

Mainly used for interaction with SPARKY

chimera

Dino

YES

This can show electrostatic maps output from delphi

dino

Povray

YES

Generates beautifully rendered images e.g. tiff's from pymol,molmol

Delphi

YES

Calculates numerous protein properties including electrostatics.

Set path in .bashrc or .cshrc to

/nfs/home/osbornem/bin.

type: delphi

APBS

YES

A non-linear Poisson-Boltzmann Solver (electrostatics!), pymol (pymike) has a plugin to use this for electrostatic calcs.

path : /nfs/home/osbornem/bin

apbs

Modeller

YES

Generate 3D coordinates based on homologous proteins

Must set path: /usr/lib/modeller8v1/bin

mod8v1

Procheck

YES

Include the following line in your .bashrc to work:

prodir=/nfs/home/osbornem/local/procheck

export prodir

alias procheck="$prodir/procheck.scr"

alias procheck_comp="$prodir/procheck_comp.scr"

alias procheck_nmr="$prodir/procheck_nmr.scr"

alias proplot="$prodir/proplot.scr"

alias proplot_comp="$prodir/proplot_comp.scr"

alias proplot_nmr="$prodir/proplot_nmr.scr"

alias aquapro="$prodir/aquapro.scr"

alias gfac2pdb="$prodir/gfac2pdb.scr"

alias viol2pdb="$prodir/viol2pdb.scr"

alias wirplot="$prodir/wirplot.scr"

procheck filename [chain] resolution

Hydronmr

YES

Calculates hydrodynamic properties of proteins, including NMR parameters such as T1, T2, t_c and ts

Set path in .bashrc or .cshrc to /nfs/home/osbornem/bin.

type: hydronmr

Reduce

YES

Among other things it can add H bonds

reduce

path : /nfs/home/osbornem/bin

HBPLUS

YES

A Hydrogen Bond calculation programme

hbplus

path : /nfs/home/osbornem/bin

NACCESS

YES

Calculates accessible area of a protein

naccess

path : /nfs/home/osbornem/bin

LIGPLOT

YES

Program for automatically plotting protein-ligand interactions

ligplot

MSMS

YES

Another molecular surface generation programme

msms

pdb_to_xyzr

pdb_to_xyzrn

path : /nfs/home/osbornem/bin

NMRPipe/

NMRDraw

YES

Scripts for corrupted 3D datasets: lpcorrupt

For example Varian Scripts click here

a tutorial I am writing can be found here

NMRPipe - automatically setup, just run your script

To run off multiple machines check here

nmrDraw (for nmrdraw)

NMRView

YES

C-version installed. Some added modules such as 2D diffusion and relaxation analyses and 4D manipulation added by mike

nmr5.4

SPARKY

Chimera

YES

YES

NMR visualizer

chimera is a molecule visualizer that goes with SPARKY

Installed by Mike: must set path in .bashrc

sparky

also ucsfdata, pipe2ucsf, vnmr2ucsf, bruk2ucsf, peaks2ucsf, matrix2ucsf

path: /nfs/home/osbornem/local/sparky/bin

ANALYSIS and FormatConverter from CCPN

YES

Analysis is an NMR visualiser and analysis programme.

FormatConverter can be used to convert and transfer NMR data from all exisitng formats. Both are form the CCPN suite of programmes.

FormatConverter

analysis

TALOS

YES

Generates Phi/Psi angles for input to structure calculations

ONLY RUNS UNDER tcsh!!!

talos.tcl -in myshifts.tab
rama.tcl -in myshifts.tab
vina.tcl -in myshifts.tab -auto

Hydronmr

YES

Calculates hyrdodynamic properties of proteins, including NMR parameters such as T1, T2, t_c and ts

Set path in .bashrc or .cshrc to /nfs/home/osbornem/bin.

type: hydronmr

Modelfree

YES

Lipari-Szabo analysis of relaxation data

path: /nfs/home/osbornem/bin

modelree

must set path first

Fast modelfree

YES

A gui based version for simplifying modelfree analysis

path: /nfs/home/osbornem/bin

First use setupFMF to set up input

Run fastMF in the same directory

must set path first

pdbinertia

r2r1_diffusion

quadric_diffusion

r2r1_tm

YES

A set of programmes used for diffusion tensor analyses

Must set correct path:

path: /nfs/home/osbornem/bin

pdbinertia

r2r1_diffusion

quadric_diffusion

r2r1_tm

RNMRTK

YES

For processing non-linear sampled datasets:

path: /nfs/home/osbornem/local/rnmrtk/rnmrtk.v3/exe

rnmrtk

COAST

YES

Useful for setting up non-linear acquisition schemes

path: /nfs/home/osbornem/bin

coast_v132.tcl

Curvefit

YES

Fitting programme for T1 T2 etc.

This has been interfaced with NMRview. I have a neat script to give a postscript output. See me about this

curvefit

CCPN

YES

cannot install these on the opterons – does work on linux box in NMR room.

FormatConverter is great for changing formats of data (restraints etc)

1D diffusion

YES

A variation of the diffusion analysis from NMRPipe

Can only use under tcsh or part of a NMRPipe script.

dosyView.tcl -tau -`cat taulist' -zoom 100.

Note taulist is a file containing the gradient strengths

2D Diffusion

YES

Installed in nmrview under analysis menu. Note you must input variables in the menu!

nmr5,4

PACKAGE

What if does

To run

Installed

Other comments

PSSI

tries to adjust chemical shifts for proper referencing

YES

xmgrace

For making graphs

xmgrace

path : /nfs/home/osbornem/bin

YES

Installed by Mike; must set path