000 Resource for ICM Scripting

YouTube

First and foremost, there is an official Molsoft channel! It is dedicated to basic GUI operations and occasionally command line trainings. If you have no idea what ICM GUI is, check this out first. It will help on learning with Mouse Clicks below.

https://www.youtube.com/channel/UC92_g6Ig0KFnlXOiy5CN1Gg

Recommended Flow

• Multi Template Modeling and Editing teaches assembly of chains without missing loop modelling. This is often the first step to look for when structures come as a multimer.

• 00:00:00 on Multimer Assembly from template hetero/homo-dimer.
• 00:33:00 on Interactive Sequence Alignment.
• 00:36:00 on imposing loop conformation by Thread Through Tether. Very useful. Skip to 00:44:00, stop at 00:48:30, No need to go through the rest. Briefly, given two intact protein substructures aligned with structurally close C- and N- parts, restraints can be placed on one substructure forcing its in-between part to adopt conformation of the aligned partnering substructure. We will do a summary on page.

• Loop Modelling teaches techniques to propose conformation(s) for a missing loop.

• 00:35:00 on Grafting. Non trivial copying of conformations.

Mouse Clicks

Perhaps, the unofficial second step to learn ICM scripting. Some mouse clicks could trigger display of underlying macros in the terminal. You may want to document these for use later on.

• Molsoft also provides written Mouse Click Tutorials

Macro

ICM Shell comes with pre-defined functions call "macro". They are written by ICM gurus. There are indeed much more macros than what listed online in manual.

• To list available macros ls macro
• To view and edit a macro, for example "wrSeqAli" edit wrSeqAli
• A lot of macros are called from s_icmhome e.g. _confGen. Simply paste s_icmhome directory to a web browser and view the script there.

Language Reference

The online Language Reference is more detailed than what is written in packaged Help Content.

• Shorter Guide to ICM Macro Functionality
• Longer Guide to ICM Scripting
• Glossary
• Forum

Language Remarks

These remarks usually concerns naming conventions

• Parameters

• nXXXXX stands for "number of". mnXXXXX stands for "maximum number of".
• http://xed.ch/h/icm.html
• https://www.molsoft.com/icm/icm-shell.html

GUI Reference

• VLS Steps