I would like to share my answer for chain separator issue for the "gmx 
do_dssp". Millions of thanks to Carsten!


The "gmx do_dssp" will output an additional line as chain separator between two 
chains. We do NOT need to provide a "ss.map" file in our working directory, and 
the command will find the default "ss.map" file automatically, and the ss.xpm 
file will have a line of "========" as the chain separator.


I created my own ss.map file based on 
http://manual.gromacs.org/online/map.html, and got the "~~~~~~~~~~" as chain 
separator, which is the same as coils. So do not do this.
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