Jul 3 2008
Contents
 
Introduction
Overview - RECOMMENDED READING FOR NEW ICM USERS
File Menu
Graphics Move Tools
Display Tab
Light Tab
Labels Tab
PDB Search Tab
Meshes Tab
View Menu
Selections
Tables
Local DB
Sequences
Bioinfo Menu
Tools Menu - Xray
Tools Menu - 3D Predict
Tools Menu - Analysis
Tools Menu - Superimpose
Homology and Modelling
Working with Chemistry Tools
Chemsitry Menu
Docking
Ligand Editor
Animations, Slides, & Documents
ActiveICM
Movie Making
Frequently Asked Questions
 FAQ-Install
 FAQ-Hardware
 FAQ-Graphics and Display
 FAQ-Structure
 FAQ-Dock
 FAQ-Cheminformatics
 FAQ-Simulations
  Movie montecarlo
  View Stack
 FAQ-Script
 Troubleshooting
Tutorial - Graphical Display
Molecular Document
Tutorial - Working with PDB Protein Structures
Tutorial - Working with Sequence Alignments
Tutorial - Ligand Binding Pocket Analysis
Tutorial - Homology and Modeling Tools
Tutorial - Crystallographic Analysis Tools
Tutorial - Working with Chemical Tables
Tutorial - Working with the Molecular Editor
Tutorial - Chemical Searching
Tutorial - Docking and Virtual Ligand Screening
 
Index
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28.7 FAQ-Simulations
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[ Movie montecarlo | View Stack ]

Frequently asked questions regarding simulations, BPMC ....

28.7.1 How do I make a movie of my montecarlo simulation and write all output.


To make a movie simply use the command :

montecarlo movie

To write all the buffered output to a file

On your UNIX command line

icm < montecarlo.scr > output.icm

where montecarlo.scr is your montecarlo ICM script

For an example of an mc script see the tutorial below.

28.7.2 How do I view a stack of solutions after a simulations?


Once any monte-carlo simulation is complete a stack of the most energetically favorable solutions is generated along with the associated energy for each element of the stack. To view this stack:

  • MolMechanics/View Stack.
  • Double click on each element in the stack (table) to load it into ICM.


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