unanswered how to draw helix with cg_secondary_structure.tcl?

  • roshanak
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8 months 3 weeks ago - 8 months 3 weeks ago #7697 by roshanak
Hi
I have a problem with cg_secondary_structure.tcl. I try to use these commands:

vmd > source cg_secondary_structure.tcl
vmd > source la.tcl
vmd > cg_helix {{1 36} {37 72} {73 108} {109 144} {145 180}} -hlxcolor "lime" -hlxrad 2.5 -hlxfilled "yes" -hlxmethod "realhelix"
( also these: vmd > cg_helix {{1 36}}"and" {{37 72}} "and" {{73 108}} "and" {{109 144}} "and" {{145 180}} -hlxmethod "cylinder" -hlxcolor "blue" -hlxrad 2 -hlxres 12
or vmd > cg_helix {{1 13} {1 13} {1 13} {1 13} {1 13}} -hlxcolor "lime" -hlxrad 2.5 -hlxfilled "yes" -hlxmethod "realhelix")


, but it does not work and it does not take a true structure. It takes a larg shapeless structure instead of 5 helix structures.
In above command {1 36} {37 72} {73 108} {109 144} {145 180} are for 5 peptides with 13 amino acid in every peptides.
I try this tcl code for other simulation with 1 peptide and it takes a helix with the additional lines in its two sides that do not remove with nopbc.
Would you please help me?
Last edit: 8 months 3 weeks ago by roshanak.

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