Release Notes for Insight 2005

This document contains changes to Insight II including enhancements to applications with new tools and functionality, and also a number of bug fixes.

Note: The most current version of these notes is maintained at the Insight 2005 web site:

http://www.accelrys.com/doc/life/insight2005/

If you are reading this from a CD installation, or a printed or older downloaded copy, this may not contain the most complete information.

Welcome to Insight II 2005, the latest release of Accelrys' premiere application for macromolecular modeling, simulation and visualization. Insight II 2005 provides a sophisticated molecular graphics environment for building and modifying molecules, molecular mechanics, molecular dynamics simulations, electrostatics, ligand design and homology modeling. This release adds new science in the form of ZDOCKpro, a program for protein-protein docking with no or minimal information about interface residues and enhancements to the CHARMm interface.

Release Media

The Insight II 2005 distribution includes the following contents:

Product. This CD contains the Insight II product and all included modules.

Gifts and Tutorials. Contains tutorial files and additional unsupported scripts and data files for all products.

Data Bank CDs. Contain library data files derived from the PDB that are required for Insight II to run protein applications such as the Biopolymer, Homology, and Binding Site Analysis modules.

Documentation. Includes the complete set of documentation for Insight II 2005, as well as that for other current Accelrys products.

Please see the file called README on the CD for installation instructions.

Platform Requirements

Red Hat Linux

The following configuration is recommended for Insight II 2005:

3.4 GHz Intel Xeon w/ EM64T

1 GB RAM

Red Hat Enterprise Linux WS 3.0 (32-bit only) running the Gnome desktop environment

Nvidia Quadro FX1300 graphics card using Nvidia Linux drivers (Driver Version)

Kernal version: 2.4.9.
Note:
Insight II is supported on Intel Pentium IV, Intel Xeon and Intel Xeon w/ EM64T processors.

Nvidia Quadro FX1100, FX1400, FX3000 and FX3400 cards are also supported.

Background jobs can be run on servers without the graphics requirements listed above. The other hardware requirements must be met.

SGI IRIX

The following configuration is recommended for Insight II 2005:

SGI IRIX 6.5.19 and above on MIPS R14000 (64-bit)

1 GB RAM

R10000 and higher systems are supported.

General

A three-button mouse is required to access the powerful mouse control functions within Insight II.

Sufficient disk space: ~2GB.

NMR Modules

The following modules are only available on SGI IRIX:

NMR Refine DGII

NMR Refine Advanced

NMR X-PLOR

CHARMm, DelPhi, Ludi, MODELER, and SeqFold can also be run on AIX servers.

Databases and Libraries

The following databases and libraries are provided with this release:

Database name

application

pdb_ca_distance.dat

Loop searching in homology and biopolymer

pdb.seq

FastA search

structure.db

Str_DB in biopolymer and b_site

database.dat

Str_DB in biopolymer and b_site

scop.1d_prf

SeqFold (SCOP db v. 1.53)

profiles.tar

Profiles-3D

Database name	application
pdb_ca_distance.dat	Loop searching in homology and biopolymer
pdb.seq	FastA search
structure.db	Str_DB in biopolymer and b_site
database.dat	Str_DB in biopolymer and b_site
scop.1d_prf	SeqFold (SCOP db v. 1.53)
profiles.tar	Profiles-3D

General Information

Insight II may occasionally require the availability of a large memory stack, therefore we suggest that you add the following line into your.cshrc file

limit stacksize unlimited

Known Issues

The following bugs are known issues at the time of shipping.

bug ID Description Workaround

05091jlnq03

You can create an assembly and form a cell around it for an explicit solvation simulation. When the original coordinates are read back into Insight II and the cell boundary remade, the assembly lies outside of the cell.

When you read back the coordinates perform the following steps

1. Go to Object | Delete, and delete the exiting assembly

2. Go to Assembly | Associate, create a new assembly containing the two objects, name the new assembly NEW_ASSEMB.

3. Rebuild the CELL:
m:Cell Assembly NEW_ASSEMB 23,23,23 90,90,90 1 Center_in_Cell

The new cell covers the whole molecule without any empty space.

05145c2sq03

Graphs saved on IRIX are not readable on Linux and vice versa.

Use on same platform on which the graph was created.

05080d3sq01

If you set up and run multiple RDOCK jobs at the same time in the same directory, the jobs all run, but only the last job run produces any results. Earlier jobs also core dump.

If you wish to run jobs simultaneously, create a separate directory for each job.

05010212301

Delphi focussing run fails when the initial coarse grid is smaller than the final grid.

Make sure that the initial coarse grid and the final grid are the same dimensions.

05076j1sq01

Insight II subwindows on Linux cannot be minimized.

Double-click the window title bar to "shade" or "roll-up" the window.

02051019001

If you do a dynamics simulation with Discover3 using rattle and then read the resulting trajectory file into DeCipher, the temperatures reported using Construct_Table are different than the temperatures reported by Discover3. This only occurs when rattle is used.

Use Discover3 to report temperatures (although this can only be done during the dynamics simulation, not in post processing a history file).

00033kjbq02

If a monomer table is sorted in some way then a new column is added (with, e.g., trajectory distance data). The order the data is entered in the column no longer coincides with the other columns.

Resort by index before creating a new column.

00060kjbq02

When exporting images at 300 DPI or above from the Plot Image window, the resulting image file may be corrupted.

Run the export once from the GUI, then rerun the command at the command line.

01102853401

Using CFF to minimize a ligand which contains an sp2 aromatic nitrogen in a ring with a hydrogen (potential is nh): the potential is correct and the oop flag is on but the hydrogen bends out of the plane.

Use restraints.

05110j1sq02

The data read in from a trajectory file (his or arc) is sometimes improperly read if the object was built in Insight II and subsequently used for the simulation.

No workaround.

05131j1sq01

Contours written out by IRIX contour from versions 2000.2 or 2005 are readable by both IRIX and Linux versions of Insight 2005. Contours written on Linux from 2000.3L or 2005 cannot be read.

Use IRIX contour to run these conversions.

05133j1sq01

Many of the engines in Insight II (fDiscover, MODELER) require the LD_ASSUME_KERNEL to be set to 2.4.9 on WS 3.0.

Before starting the Insight II program (or either of these engines in standalone mode), issue the following UNIX command: setenv LD_ASSUME_KERNEL 2.4.9 Or you can add this command to your .cshrc file.

05112j3tq01

In Profiles_3D, when you execute Create_Profile with "*" in the PDB File box, the job fails and reports a segmentation fault in the log file.

The PDB_PREFIX and PDB_SUFFIX environment variables can be used to control how wildcard files are searched for.

setenv INSIGHT_PDB <pdbfilesdir>

setenv PDB_PREFIX ""

setenv PDB_SUFFIX ".pdb"

(or ".gz" as needed)

05118d3sq03

When you specify a relative path for a ZDOCK output file, you must return to the run directory to load the file. Attempting to load the file from the previously specified directory results in an error.

Do not specify a relative path. The file is written to the local run directory. If you wish to write to a different directory, change your working directory and run the job.

05146gxmq01

On the IBM T42p ThinkPad, the redraw performance of the OpenGl window drops off when a dialog is open and overlapped with it. Also, when a dialog is moved around on top of the OpenGL portion of the application, there is delay (a wait cursor is shown) before the application becomes responsive again. This behavior was not observed on machines with NVidia graphics.

--

05124j1sq02

Trying to detach a CDiscover job from Insight II on Linux results in a job failure.

--

05049cbug01

Subwindows on IRIX cannot be minimized.

--

bug ID	Description	Workaround
05091jlnq03	You can create an assembly and form a cell around it for an explicit solvation simulation. When the original coordinates are read back into Insight II and the cell boundary remade, the assembly lies outside of the cell.	When you read back the coordinates perform the following steps 1. Go to Object \| Delete, and delete the exiting assembly 2. Go to Assembly \| Associate, create a new assembly containing the two objects, name the new assembly NEW_ASSEMB. 3. Rebuild the CELL: m:Cell Assembly NEW_ASSEMB 23,23,23 90,90,90 1 Center_in_Cell The new cell covers the whole molecule without any empty space.
05145c2sq03	Graphs saved on IRIX are not readable on Linux and vice versa.	Use on same platform on which the graph was created.
05080d3sq01	If you set up and run multiple RDOCK jobs at the same time in the same directory, the jobs all run, but only the last job run produces any results. Earlier jobs also core dump.	If you wish to run jobs simultaneously, create a separate directory for each job.
05010212301	Delphi focussing run fails when the initial coarse grid is smaller than the final grid.	Make sure that the initial coarse grid and the final grid are the same dimensions.
05076j1sq01	Insight II subwindows on Linux cannot be minimized.	Double-click the window title bar to "shade" or "roll-up" the window.
02051019001	If you do a dynamics simulation with Discover3 using rattle and then read the resulting trajectory file into DeCipher, the temperatures reported using Construct_Table are different than the temperatures reported by Discover3. This only occurs when rattle is used.	Use Discover3 to report temperatures (although this can only be done during the dynamics simulation, not in post processing a history file).
00033kjbq02	If a monomer table is sorted in some way then a new column is added (with, e.g., trajectory distance data). The order the data is entered in the column no longer coincides with the other columns.	Resort by index before creating a new column.
00060kjbq02	When exporting images at 300 DPI or above from the Plot Image window, the resulting image file may be corrupted.	Run the export once from the GUI, then rerun the command at the command line.
01102853401	Using CFF to minimize a ligand which contains an sp2 aromatic nitrogen in a ring with a hydrogen (potential is nh): the potential is correct and the oop flag is on but the hydrogen bends out of the plane.	Use restraints.
05110j1sq02	The data read in from a trajectory file (his or arc) is sometimes improperly read if the object was built in Insight II and subsequently used for the simulation.	No workaround.
05131j1sq01	Contours written out by IRIX contour from versions 2000.2 or 2005 are readable by both IRIX and Linux versions of Insight 2005. Contours written on Linux from 2000.3L or 2005 cannot be read.	Use IRIX contour to run these conversions.
05133j1sq01	Many of the engines in Insight II (fDiscover, MODELER) require the LD_ASSUME_KERNEL to be set to 2.4.9 on WS 3.0.	Before starting the Insight II program (or either of these engines in standalone mode), issue the following UNIX command: setenv LD_ASSUME_KERNEL 2.4.9 Or you can add this command to your .cshrc file.
05112j3tq01	In Profiles_3D, when you execute Create_Profile with "*" in the PDB File box, the job fails and reports a segmentation fault in the log file.	The PDB_PREFIX and PDB_SUFFIX environment variables can be used to control how wildcard files are searched for. setenv INSIGHT_PDB <pdbfilesdir> setenv PDB_PREFIX "" setenv PDB_SUFFIX ".pdb" (or ".gz" as needed)
05118d3sq03	When you specify a relative path for a ZDOCK output file, you must return to the run directory to load the file. Attempting to load the file from the previously specified directory results in an error.	Do not specify a relative path. The file is written to the local run directory. If you wish to write to a different directory, change your working directory and run the job.
05146gxmq01	On the IBM T42p ThinkPad, the redraw performance of the OpenGl window drops off when a dialog is open and overlapped with it. Also, when a dialog is moved around on top of the OpenGL portion of the application, there is delay (a wait cursor is shown) before the application becomes responsive again. This behavior was not observed on machines with NVidia graphics.	--
05124j1sq02	Trying to detach a CDiscover job from Insight II on Linux results in a job failure.	--
05049cbug01	Subwindows on IRIX cannot be minimized.	--