002 Selecting Atom, Variable and Energy

There are two main types of Attribute and Selection in ICM, namely Atom and Variable. We will go through them one by one.

Atom

As its name suggest the unit of reference is each atom in an ICM/non-ICM object. Below we consider current object i.e. a_.

Atom Selection

The major reference for atom selection can be found at Language Manual Below I have categorised some useful lines.

Secondary Structure

Require assignment of ss in icm object. Note DSSP Labels.

• a_/SH All helices
• a_/SEH All sheets and helices
• a_/S_ All coils
• a_/SEH&a_//ca&a_/510:533 All helices ca in region 510 533. These are done through &.
• a_.d select chain d of all available object
• a_.d [1] select chain d of first object. Equivalent to a_1.d

Residues

• a_/T terminal residues (like N-terminal, C-terminal, and DNA 5' and 3' termini).

Editing Atom Attribute

With proper atom selection, we can now change selected atom attributes

Residue Number

Simple command to renumber residues of a chain. Unlike other softwares where residues sharing the same residue number is strictly intolerable, ICM will relabel those overlaping residues as e.g. 518 vs 518a to allow coexistence. This arise usually when user simply cut and paste from another structure and made their PDB files.

• align number a_5w0pNoT506End.PTH1R/1:535 27

Atom Name / Coordinates

Variable

Variable selection

Editing Variable Attribute

Energy

• A list of possible energy terms can be viewed by mouse clicking MolMechanics>EnergyTerms...>
• Printing energy show energy