PACKAGE

What if does

To run

Installed

Other comments

NMRPipe/

NMRDraw

Nmr processing

NMRPipe - automatically setup, just run your script

To run off multiple machines check here

nmrDraw (for nmrdraw)

YES

Scripts for corrupted 3D datasets: lpcorrupt

For example varian Scripts click here

a tutorial I am writing can be found here

NMRView

NMR visualizer and analysis

C-version installed. Type
nmr5.4

YES

Mike has many scripts to help analysis. Ask him

CNS

Structure Calculation

cns_solve1.1

USE SGE TO RUN

YES

XPLOR-NIH

NIH version of xplor

xplor

USE SGE TO RUN

YES

current version 2.11

to run on many cpus

VMD-XPLOR

Visualiser for XPLOR/CNS

vmd-xplor

path: /nfs/home/osbornem/local/vmd-xplor-1.4-Linux_2.4_i686

YES

Installed by Mike: must set path in .bashrc

ARIA

Structure Calculations

for Aria1.1 setup
Aria1.2: setup

For runing on multiple machines

Aria2.0 not yet working

RUN USING SGE

YES

Installed by Mike

versions available are:
Aria1.1
Aria1.2

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

CYANA

Structure Calculations

cyana2

NO

not well documented. Some examples here

TALOS

Generates Phi/Psi angles

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

YES

To get a "myshifts.tab" file you can use NMRView.

Only runs in tcsh shell

SPARKY

Chimera

NMR visualizer

chimera is a molecule visualiser that goes with SPARKY

sparky

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

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

YES

Installed by Mike: must set path in .bashrc

calcdiff

for diffusion analysis

/usr/local/calcdiff.s

NO

see here for instructions

CSI

chemical shift index

csi

NO

script for conversion from NMRView format

PROCHECK

Checks for good structures

procheck

YES

CCPN

Data model system

FormatConverter

NO

Useful for changing data formats

PYMOL

Visualisation - good for movies

pymol.com

YES

Some example mpeg mpeg1 and a high res avi (WARNING - BIG FILE) movies I made using PYMOL

PYMOL

Loads of add-ons for movies, electrostatics via apbs

/nfs/home/osbornem/pymol-0.98/pymol.mike

YES
station05

Installed by Mike. Apbs (for electrostatics) will only work on Station05

MOLMOL

Visualisation

molmol

YES

Modelfree

Dynamics analyis using modelfree

modelfree4
path: /nfs/home/osbornem/bin

YES

Installed by Mike: must set path in .bashrc

Fast modelree

A gui based version for simplifying modelree

First use setupFMF to set up input

Run fastMF in the same directory

path: /nfs/home/osbornem/bin

YES

Installed by Mike: must set path in .bashrc

pdbinertia

r2r1_diffusion

quadric_diffusion

r2r1_tm

A set of programmes used for diffusion tensor analysis

pdbinertia

r2r1_diffusion

quadric_diffusion

r2r1_tm

path: /nfs/home/osbornem/bin

Yes

Installed by Mike: must set path in .bashrc

RNMRTK

processing with maximum entropy

rnmrtk

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

YES

Installed by Mike: must set path in .bashrc

COAST

helps produce processing scripts for RNMRTK

coastv132.tcl

YES

Station05

I am testing how well this works with the authors

Curvefit

T1/T2 curve fitting

curvefit

YES

Station05

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

PSSI

tries to adjust chemical shifts for proper referencing

YES

Modeller

modelling package

mod8v1

path: /usr/lib/modeller8v1/bin/

YES

Station05

Installed by Mike: must set path

Reduce

Adds/subtracts H's from pdb files

reduce

path : /nfs/home/osbornem/bin

YES

Installed by Mike: must set path

xmgrace

For making graphs

xmgrace

path : /nfs/home/osbornem/bin

YES

Intsalled by Mike; must set path

DINO

Viewing maps

dino

YES

Intsalled by Mike; must set path

APBS

calculating electrostatic surfaces

apbs

path : /nfs/home/osbornem/bin

YES

Intsalled by Mike; must set path

HBPLUS

calulates h-bonds

hbplus

path : /nfs/home/osbornem/bin

YES

Intsalled by Mike; must set path

ACCESS

calulates accessible surface area

naccess

path : /nfs/home/osbornem/bin

YES

Intsalled by Mike; must set path

MSMS

calulates accessible surface area

msms

pdb_to_xyzr

pdb_to_xyzrn

path : /nfs/home/osbornem/bin

YES

Intsalled by Mike; must set path

LIGPLOT

Identifies interaction

ligplot

YES