Jmol as editor

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Although Jmol is by design a viewer for molecular structures, its growth has brought some limited capabilities for editing the model. By editing, we mean altering atom positions or identities (e.g. chemical element), addition or removal of some atoms.

Modifying bonds

set autoBond defines whether Jmol will add bonds based on interatomic distances (for file formats that do not specify bonds).

connect allows to add or delete bonds arbitrarily, or to change bond order.

calculate hBonds makes Jmol calculate a limited set of likely hydrogen bonds.

calculate aromatic reassigns all bonds of aromatic type as alternating single and double aromatic bonds.

calculate structure does not really change bonds, but assignation of secondary structure for proteins and, hence, cartoon/ribbon rendering and coloring by structure.

Moving atoms

translateSelected changes atom coordinates according to some XYZ values (or fractional crystallographic coordinates).

rotateSelected changes atom coordinates applying a rotation operation.

invertSelected changes atom coordinates applying a symmetry operation.

minimize changes atom coordinates following a force field calculation in search of a conformation of minimal energy.

See also section How to change atom coordinates in the mouse manual.

Adding atoms

data allows to add atoms and to add or redefine atom-associated properties (such as coordinates, charge, radius, temperature factor, occupancy, vibration, etc., or custom properties).

calculate hydrogens allows to add hydrogen atoms, at reasonable positions, in models that lack them. An energy minimization may be convenient afterwards, or you can use the special minimize addHydrogens command to do both in one go.

Removing atoms

zap allows to delete all atoms in a certain model/frame.

PDB file editing with Jmol

  • PDB file editing with Jmol. How to put the loaded PDB file into an array of lines, edit those lines with Jmol commands, and write a new PDB file. Also how to put Jmol commands in REMARK lines in the headers of PDB or PNGJ files.