[gmx-users] Why the '5-Helix' randomly displayed in the scount.xvg after running do_dssp?

[Erik Marklund]

Dear Cheng,

Gromacs is open source. Implement this at your own will. If there is a sufficient interest in such a feature it might even have a place in the official release at some point.

Kind regards,
Erik
______________________________________________
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 22 Feb 2018, at 18:19, ZHANG Cheng <272699575 at qq.com<mailto:272699575 at qq.com>> wrote:

Dear Gromacs,
The scount.xvg file was obtained after running


echo 1 | gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns


The secondary structures listed are:
'Structure','Coil','B-Sheet','B-Bridge','Bend','Turn','A-Helix','3-Helix','5-Helix'


I ran the command for different proteins. It surprised me that the last '5-Helix' randomly displayed in the scount.xvg. Maybe some proteins did not have the '5-Helix', but why not just show them as 0? Can this be improved?


Because I am using a script to read the scount.xvg files, so I want all the files have the same format.


Thank you.


Yours sincerely
Cheng
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