From: Tristan Croll (
Date: Thu Jan 21 2016 - 02:41:42 CST

I know the newer ones are better, but I still use this on occasion when I just want to quickly align two structures... anyway, it breaks down once the molid passes 999. The offender is line 510 of rmsd.tcl:

    $pdb_list insert end [format "%-4s%-10s" [molinfo index $i] [molinfo $i get name]]

Once the molid hits 4 characters, downstream procs read the molid and name as a single entry.