Insight II
by Accelrys, Inc
Insight II is a user-friendly graphical molecular modelling program developed by Accelrys Inc. (formerly a product of MSI and BIOSYM) that
incorporates a variety of useful molecular modelling codes specifically designed for biological systems, including metal containing systems.The
Laboratory for Molecular Simulation, in collaboration with the departments of chemistry, biochemistry/biophysics, and chemical
engineering, has purchased licenses for a large number of the modules available in insightII. If you are a researcher at Texas A&M University and
are interested in obtaining access to this software, want to test a module that we currently do not have a license for, or simply have questions about
the software, please contact
Lisa M. Pérez
The current release of Insight II is version 2005 and runs on both IRIX and Linux Platforms.
To run InsightII 2005 you will need the following lines in your .tcshrc file:
alias i2005 'source /chem/insight/cshrc;insightII'
To run older versions of Insight II you will need to add additional aliases:
alias iversion 'source /chem/insight/cshrc.version;insightII'
Where
version should be set to one of the older versions of insight available: 400, 980, I2000, I2000.2, I2000.3L
versions 400, 980, I2000, and I2000.2 are SGI/IRIX versions only
versions I2000.3L is a Linux only version
For example, to run version 400, you would need to add the following alias to your .tcshrc file:
alias i400 'source /chem/insight/cshrc.400;insightII'
Useful handouts for insightII in pdf format
Exporting images from insightII
Notes for the Linux version of InsightII:
InsightII 2000.3L and Insight 2005 are not supported under the bash shell. If your linux account has bash as its default shell (as most
linux accounts are), you must enter the t-shell by typing tcsh at the prompt before executing the i2005 or i2000.3L command. You can also
use the command chsh to change your default shell to tcsh or have your administrator change your default shell to tcsh. Changing your shell
to tcsh on a linux machine may cause problems when you try to run other programs.
The linux version of InsightII has some specific hardware requirements if you wish to use hardware stereo
and operating system requirements if you want technical support. Please see the
technical section below for more information.
For more information about InsightII and the modules listed below, please visit:
Insight II homepage
or
Insight II documentation The InsightII documentation link will ask for a
username and password. If you are a researcher at Texas A&M University and would like access to the documentation, please e-mail a request for the username and
password to
Lisa M. Pérez
Modules Available For Use Through The LMS
| Module Name | Number of Licenses |
| Affinity | 1 |
| bioplymer | 4 |
| CHARMm | 1 |
| Characterize* | 1 |
| CFF Force Field | 2 |
| Delphi | 1 |
| Diffraction | 1 |
| Discover | 12 |
| DMol | 4 |
| DSolid | 1 |
| ESOCS | 1 |
| Fast Structure | 1 |
| Felix Assign | 2 |
| Felix Model | 3 |
| Felix ND | 3 |
| Homology | 2 |
| Insight II | 16 |
| Modeler | 1 |
| NMR Refine Advanced | 2 |
| NMR Refine DGII | 3 |
| Plane Wave | 1 |
| QuantaMM | 1 |
| Sketcher/Converter | 1 |
| Solids builder* | 2 |
| Solids Diffusion* | 1 |
| Solids Docking* | 1 |
| Solids NMR* | 1 |
| Solids Simulation* | 1 |
| Soption | 1 |
| Turbomole | 1 |
*Only available in Insight 4.0.0 P+
For a brief description of the modules availble for Insight II, please visit the
Insight II homepage
Trouble-Shooting:
If you receive the error: i2005 - command not found
you need to check the alias in your .tcshrc file to make sure that it is properly defined.
If you receive the error: /chem/insight/cshrc not found
you should check to see if the /chem directory has been mounted on your machine by typing
df at the prompt.
If /chem is not listed in the column under 'Mounted on', it is not mounted on your machine you will need to mount it before you
can run the cerius program.
If /chem has been mounted on your machine in the past you will need to login as root and type the following command:
/sbin/mount -a
if this does not mount /chem (type df to determine if /chem is mounted) check to make sure that you have the following line in your /etc/fstab file:
SGI/IRIX:
chmsgi.chem.tamu.edu:/chem /chem nfs soft,intr,bg,vers=2 0 0
Linux:
chmsgi.chem.tamu.edu:/chem /chem nfs defaults 0 0
If this line is in your fstab file and you still cannot mount /chem on your machine, contact your system administrator.
If you are running on a remote machine and you receive the error:
Xlib: connection to "labmol4.chem.tamu.edu:0.0" refused by server
Xlib: Client is not authorized to connect to Server
Error: Can't open display:labmol4.chem.tamu.edu:0.0
(where labmol4.chem.tamu.edu will be replaced by the local machine name)
You need to use X11 forwarding to access the remote machine (ssh -X
username@
remote_machine_name or you may also need to use the -Y flag
ssh -X -Y
username@
remote_machine_name )
Technical Section for Linux version of insightII
Hardware requirements for the linux version of InsightII:
Intel-compatible workstations running Red Hat Enterprise Linux (RHEL) WS 2.1, WS 3.0 and WS 4.0 (see Patch) on Intel x-86 and EM64T processors (32-bit OS only)
IBM Intellistation Z-Pro 6223-28U & 6223-29U are recommended.
Insight II 2005 on Linux is certified on the following graphics cards by Nvidia with appropriate Nvidia drivers: Quadro4 980 XGL, FX1100, FX1300/1400, FX3000, FX3400
NMR Refine DGII, NMR Refine Advanced, and NMR X-PLOR are not supported on Linux.
Insight II 2005 is now also supported IBM T42p Thinkpads running Linux WS 3.0 and the FireGL2 T2 graphics card with appropriate drivers from ATI.
Some tools, for example CHARMm, also run on IBM AIX.
Software requirements for the linux version of InsightII:
compat-libstdc++. Insight II 2005 on Red Hat Enterprise Linux requires the compat-libstdc++ RPM.
If this RPM is not installed, the you may see an error such as:
/usr/accelrys/I2005/Linux_2_Intel_32/biosym_exe/splash: error while loading shared libraries:
libstdc++-libc6.2-2.so.3: cannot open shared object file: No such file or directory
The version of this RPM that is packaged with Red Hat Enterprise Linux 3.0 WS Update 4 is compat-libstdc++-7.3-2.96.128.i386.rpm.
openmotif21. Insight II 2005 on Red Hat Enterprise Linux requires the openmotif21 RPM.
If not installed, the user may see an error such as:
Loading Insight II using OpenGL graphics ...
/usr/accelrys/I2005/Linux_2_Intel_32/biosym_exe/insightII: error while loading shared libraries:
libXm.so.2: cannot open shared object file: No such file or directory
The version of this RPM that is packaged with Red Hat Enterprise Linux 3.0 WS Update 4 is openmotif21-2.1.30-8.i386.rpm
detailed requirements
You will need a username and password for this site. Please e-mail
Lisa M. Pérez for the username and password.
