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002 Selecting Atom, Variable and Energy

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Jordy Homing Lam edited this page Jan 26, 2023 · 12 revisions

There are 3 main types of Attribute and Selection in ICM, namely Atom, Variable and Energy. 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).

Keyword Search

Residue Type

  • a_A peptides and proteins
  • a_S sugars
  • a_W water including deuterated water (dod)
  • a_H hetatm, usually ligands and water molecules
  • a_L lipids
  • a_M Metals
  • a_N nucleic acids
  • a_U unknown All the rest untyped.

Size Characteristics

  • a_J3:5 number of residues filter, e.g. a_J3:5 3 to 5 residues residues
  • a_O3[:5] number of real atoms filter, e.g. a_O3 for more than 3 atoms

Icm Linked

  • a_K molecules with linked sequence alignment
  • a_Q molecules which have a seQuence linked to them

Chain ID

  • a_C select by Chain, e.g. a_1.Cabc , use underscore ('_') for space.

PDB Attribute

  • a_B molecules included in Biological unit

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

Resname

a_/cys - all cysteine

Select on screen

as_graph = a_

Variable

General Syntax

These can be used with keywords below

  • V_ All possible variables.
  • v_ All unfixed variables.

Selection

These can be done as free or possible variables e.g. v_B or V_B

  • V_B All bond lengths.
  • V_A All bond angles. (Not torsion angles)
  • V_T All torsion angles

Editing Variable Attribute

Assign restraint

Energy

  • A list of possible energy terms can be viewed by mouse clicking MolMechanics > EnergyTerms...
  • Printing energy breakdown show energy
  • Weighing different energy terms by global dcWeight = 2000.0
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