I am working on molecular dynamic simulation of prion protein. I've DSSP file of this protein by the “program DSSP, CMBI version by M.L. Hekkelman/2010-10-21ˮ but I can᾿t determine the percentage of its secondary structure. If there is an answer, I would be grateful.
The gromacs tool do_dssp (freeware) uses the dssp program for a graphical output. In it's -cs output (scount.xvg) it gives you the secondary structure in the following form:
@ s0 legend "Structure"
@ s1 legend "Coil"
@ s2 legend "B-Sheet"
@ s3 legend "B-Bridge"
@ s4 legend "Bend"
@ s5 legend "Turn"
@ s6 legend "A-Helix"
@ s7 legend "5-Helix"
@ s8 legend "3-Helix"
# SS % 0.67 0.17 0.13 0.01 0.11 0.16 0.38 0.00 0.05
The gromacs tool do_dssp (freeware) uses the dssp program for a graphical output. In it's -cs output (scount.xvg) it gives you the secondary structure in the following form:
@ s0 legend "Structure"
@ s1 legend "Coil"
@ s2 legend "B-Sheet"
@ s3 legend "B-Bridge"
@ s4 legend "Bend"
@ s5 legend "Turn"
@ s6 legend "A-Helix"
@ s7 legend "5-Helix"
@ s8 legend "3-Helix"
# SS % 0.67 0.17 0.13 0.01 0.11 0.16 0.38 0.00 0.05
Is this last line, #ss% is multiplied by 100 or this is the final percentage? The summation of this count gives 1.68 , so what happend to the rest of 98.32?
- Badges
- Science topic