The ISOLDE Command Line

While the primary mode of control of ISOLDE is via The ISOLDE GUI, if you prefer you can also perform many tasks via the command line, such as launching the GUI (isolde start), starting, stopping and pausing simulations (isolde sim), and performing basic manipulations (isolde pepflip and isolde cisflip). Some functions are currently available only through the command line - in particular, Adaptive Distance Restraints.

isolde tutorial

Brings up the ISOLDE Tutorials help page, providing interactive case studies for working on models in ISOLDE.

isolde demo

Syntax: isolde demo demoName [modelOnly true/false] [startIsolde true/false]

Primarily intended for use with the ISOLDE tutorials. Loads saved atomic coordinates for use in rebuilding.

demoName: either “cryo_em” or “crystal”

modelOnly: if true, load only the model and not the electron density map

startIsolde: if true, the ISOLDE GUI will be started.

isolde start

Brings up The ISOLDE GUI. The first model in the list of open models will be automatically prepared with ISOLDE’s default visualisation mode. This also sets the display camera to orthographic projection and lighting to simple. It is strongly recommended that you do not change these settings during your ISOLDE session.

isolde sim

Syntax: isolde sim cmd [atoms] [discardTo discardTo]

Start, stop or pause an interactive simulation.

isolde sim start [atoms]

Launches the ISOLDE GUI if not already running, and starts a simulation. If no atoms are specified, the simulation will encompass the entirety of the current selected model (or the first open model if ISOLDE is not already running). If atoms is specified, the selected atoms must come from a single model (if this is not the current selected model, ISOLDE will automatically switch).

isolde sim stop [discardTo discardTo]

discardTo: one of “checkpoint” or “start”

Stop the currently running simulation, and optionally discard the results. If discardTo is not specified, the current state of the model will be kept. Otherwise, the atomic positions and states of all restraints will be reverted either to the starting state or the last saved checkpoint.

isolde sim pause

Pauses/resumes the current simulation.

isolde pepflip

Syntax: isolde pepflip atoms

Attempt to flip the peptide bond N-terminal to each selected residue, starting a suitable simulation if none is currently running. Requires ISOLDE to already be initialised. Residues outside the model currently selected for ISOLDE (or outside the mobile selection if a simulation is running) will not be flipped.

isolde cisflip

Syntax: isolde cisflip atoms

Attempt to flip the peptide bond N-terminal to each selected residue from cis to trans or vice versa, starting a suitable simulation if none is currently running. Requires ISOLDE to already be initialised. Residues outside the model currently selected for ISOLDE (or outside the mobile selection if a simulation is running) will not be flipped.

isolde ignore

Syntax: isolde ignore residues

Tell ISOLDE to ignore a selection of residues in future simulations. This will not take effect until the next simulation is started. Ignored residues will still be used for structure factor calculations, but do not take part in simulations in any way. Atoms directly bonded to an ignored residue will be fixed in space. This command is most useful in dealing with severe clashes that are otherwise intractable (e.g. docked homology models with intertwined loops):

  • select one of the clashing chains

  • isolde ignore sel to ignore it

  • start a simulation and remodel its counterpart into density

  • stop the simulation, then isolde ~ignore to clear the list of ignored residues

  • if necessary, ignore the selection you just remodelled and run a simulation to fix the other side of the problem area

  • stop any running simulation, isolde ~ignore, then run a final simulation with everything included to resolve any remaining clashes.

isolde ~ignore

Syntax: isolde ~ignore residues

Tell ISOLDE to stop ignoring a selection of residues for simulation purposes. This will not take effect until the next new simulation is started.

isolde restrain distances

See Adaptive Distance Restraints

isolde release distances

See Adaptive Distance Restraints

isolde adjust distances

See Adaptive Distance Restraints