Overview

We have two computer labs consisting of 19 workstation-class Linux computers with access to many data processing and structure analysis programs for NMR spectroscopy, CryoEM, and X-ray crystallography. Scientific software environments and versioning are managed with environment modules.  These computers and software are available to all of the faculty and students in our department.

Access

Access to all linux computers in the department is via centralized LDAP.  If you do not already have a Structbio login, contact the Systems Administrator.  Storage is provided via centralized NFS home directories, meaning you can login with your credentials to any linux computer and access your files.

If you are doing a lot of disk-intensive data processing, use the local /data partition to process your data and then copy it back to your network home folder.  This reduces strain on the network.  Note that /data is local to each workstation and is not backed up.

Environment Modules

Environment modules enable users to easily load application environments, for example to use one of the applications below.  Environment modules should be used wherever possible instead of editing startup scripts, as they will make the environment more consistent and enable you to access new versions as they become available.

To get a list of available modules: module avail
To load a module: module load method/program/version

For example, to load the cryoem application “Chimera” version 1.10.1, you would type:  module load cryoem/chimera/1.10.1

Once the module is loaded, you can run all commands associated with that software package.

Available Application Software

NMR
alis
amber10
amber11
aqua
blast
ccpnmr
cns
cns solve
csrosetta
curvefit
cyana
delphi
dssp
grasr
haddock
hmsIST
istHMS
jufo
MGLTools
modeller9
montenmr
NAMD
nmrfam-sparky
NMRPipe
nmrview
nmrviewj
pales
procheck
profit
psipred
RCI
reduce
rosetta31
vmd
X3DNA
xplor-nih

X-RAY Crystallography
adxv
arp/warp
ATSAS
bnp
bobscript
ccp4
cns
cns_solve
coot
crystfel
DELPHI
D*TREK
ENSEMBLE
HKL2000
molscript
PHASES
phenix
rave
ribbons
shelx
solve
Structure Studio
XDS
XRayView
xutil

CryoEM
auto3dem
bsoft
chimera
ctf
em2em
EMAN
EMAN2
emip
i3
IHRSR
image2000
IMOD
koji
laser
PArticle
protomo
relion
spiderweb
tomo-tools
UROX
x3d
Xmipp