VMD User's Guide

to turn off material characteristics for all objects in VMD). One surprising effect of materialcharacteristics is that lines are affected. In some lighting situations, the lines can even appearto disappear. Thus, you may want to turn off materials before drawing lines.• material : Sets the material to use for the corresponding graphics molecule. namemust be a valid material name, as displayed in the Materials menu.• delete id: Deletes the graphics primitive with the given id.• delete all: Deletes all graphics primitives.• replace id: Causes the next graphics primitive to replace the one with the given id. Subsequentgraphics primitives will be added to the end of the list as usual.• exists id: Returns whether the primitive with the given id exists.• list: Returns a list of valid graphics id’s.• info id: Returns the text of a Tcl command which will recreate the graphics primitive withthe given id.8.3.10 gettimestepRetrieve the specified molecule’s timestep as a Tcl byte array which can be used for high-efficiencyanalysis calculations by compiled Tcl plugins.• < molid> < timestep >: retrieve timestep as a Tcl byte array for use in compiled analysisplugins.8.3.11 helpDisplay the on-line help file with an HTML viewer. See Chapter 12 for information on how tochange the default viewer (which is Netscape).• [ subject]: Jump to help corresponding to subject.Presently, “subject” can be any one of the following words, which launches the associated URL.To guarantee that the help system will work correctly, you will probably want to start up yourweb browser before choosing one of these options. After you do this, VMD will properly direct thebrowser to the pages mentioned below.8.3.12 imdControls the connection to a remote simulation.• connect host port: connect to an MD simulation running on the machine named host andlistening on port port. This command will fail if a previously-established connection has notyet been disconnected.• detach: Disconnect from the simulation; the simulation will continue to run.100