[gmx-users] chain separator issue for the "gmx do_dssp": do NOT need to provide a "ss.map" file

[ZHANG Cheng]

Also, can the "map file format" page be updated with "chain separator"?
http://manual.gromacs.org/online/map.html




9
~                  Coil           1           1           1
E               B-Sheet           1           0           0
B              B-Bridge           0           0           0
S                  Bend           0         0.5           0
T                  Turn           1           1           0
H               A-Helix           0           0           1
I               5-Helix         0.5           0         0.5
G               3-Helix         0.5         0.5         0.5
=       Chain_Separator         0.9         0.9         0.9





------------------ Original ------------------
From:  "ZHANG Cheng"<272699575 at qq.com>;
Date:  Fri, Apr 6, 2018 10:13 PM
To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;"ZHANG Cheng"<272699575 at qq.com>;

Subject:  chain separator issue for the "gmx do_dssp": do NOT need to provide a "ss.map" file



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.