mxpix 2100 dev xwindows ax a m \Then set the environment variable MOL_START to point to this file. You could put this in your .login if you are going to use it much. Once set, this file will be run as part of the entry to molly. Concatenated commands or calls to other files are possible in the startup file which is just a file of commands like any other.
molly will also look for a local startup file called molly.com in whichever directory you are working in. This allows you to define a set of commands/settings suited to a particular dataset.
A feature that you may want to change is the normal molly assumption of the extension ".mol". This can be turned on/off with molex . Similarly clobber can be used to make molly overwrite files on output or not as the case may be.