As far as I'm aware the process is similar to retail HL2 but not the same.
You need to decompile the model using Crowbar or a HL2BETA-specific mdl-decompiler.
Then you can import the SMDs into an animation tool like Blender, and add a sequence with said animation to the QC generated by crowbar when decompiling.
As for compiling the model after all of that, please see
this thread on this forum, it should help.