[gmx-users] Secondary structure of peptides
jalemkul at vt.edu
Wed May 9 02:44:16 CEST 2018
On 5/7/18 10:57 PM, m g wrote:
> Dera Justin,I tried to obtained .eps file for my peptides with this command "gmx xpm2ps -f ss.xpm -o ss.eps -bx 1 -by 30", but unfortunately I can't obtained a good .eps file that show me the secondary structure. I tried another value for -bx and -by flags, but they can't gave me a good figure. Basically,how should I choose values for -bx and -by flag? Would you please help me?Best regards,Ganj
You need to calculate a conversion factor that converts the ratio of (#
of frames/# residues) to something legible. You may be better off using
an .m2p file, which gives you lots of options for tweaking the output.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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