setup-vmd

The setup-vmd subcommand configures VMD to load pestifer’s Tcl library automatically on startup.

$ pestifer setup-vmd

This writes ~/.pestifer/vmd_init.tcl with the absolute path to pestifer’s Tcl root hardcoded, and appends a one-line source hook to ~/.vmdrc:

# pestifer setup-vmd
if {[file exists ~/.pestifer/vmd_init.tcl]} { source ~/.pestifer/vmd_init.tcl }

The hook in ~/.vmdrc never needs to change between pestifer versions. After upgrading pestifer or switching conda environments, simply re-run pestifer setup-vmd to regenerate ~/.pestifer/vmd_init.tcl with the updated path.

Important

Run pestifer setup-vmd from the conda environment in which pestifer is installed so that the correct installation path is recorded. VMD itself can be launched from any environment.

Once set up, VMD automatically loads pestifer’s Tcl library on startup, including extended definitions of the glycan and lipid atomselect macros and all PestiferUtil procedures.