VMD User's Guide

– autobonds : Turn automatic bond calculation on/off. This can be useful forloading unusual non-molecular coordinates for which VMD’s bond-finding algorithm istoo slow (e.g., if the point density is very high). Default is on.– molid: For addfile only. The molecule id of the molecule into which the file should beloaded may be specified. It must be the last option specified. If omitted, the default isthe top molecule.• load structure file type structure file [coordinate file type coordinate file] : Load a new moleculefrom filename(s) using the given format. If an additional coordinate file is specified, load thisfile as well. New in VMD 1.8: All frames from the coordinate file will be loaded beforethe command returns. If this is not desirable, use the animate read command for more finegrainedcontrol over how coordinate files are loaded. Previous version of VMD loaded onlyone frame before returning. The function will return the id of the newly created molecule, orreturn an error if unsuccessful.• urlload : Load a molecule of file type from a given URL address. Returnthe id of the newly created molecule, or an error if unsuccessful.• pdbload : Retrieve the PDB file with the specified accessioncode from the RCSB web site. Returns the id of the newly created molecule, or an error ifunsuccessful.• list: Print a one-line status summary for each molecule.• list molecule number: Print a one-line status summary for each molecule matching themolecule number. If only one molecule matches the molecule number, also print the representationstatus for this molecule, i.e., number of representations as well as the representationnumber, coloring method , representation style and the selection string for each of therepresentations.• color coloring method: Change the default atom coloring method setting.• representation rep style: Change the default rendering method setting.• selection select method: Change the default atom selection setting.• clipplane center clipplane id rep number molecule number [ vector ]• clipplane color clipplane id rep number molecule number [ vector ]• clipplane normal clipplane id rep number molecule number [ vector ]• clipplane status clipplane id rep number molecule number [ boolean ]• modcolor rep number molecule number coloring method: Change the current coloring methodfor the given representation in the specified molecule.• modmaterial rep number molecule number material name: Change the current material forthe given representation in the specified molecule.• modstyle rep number molecule number rep style: Change the current rendering method(style) for the given representation in the specified molecule.108