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unanswered Visualization of dimer in VMD - cg_helix fails

  • pakyriak
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7 years 2 months ago #7087 by pakyriak
Visualization of dimer in VMD - cg_helix fails was created by pakyriak
Hello,

I have a peptide dimer embedded in a bilayer and I am trying to visualize it using the cg_secondary_structure script. I believe that the issue is that I cannot specify for which peptide I am giving the helix information.
i.e. my first peptide had 33 aminoacids and the second 34.
I tried using commands like cg_helix {{5 30} {2 32}}, or just one cg_helix {{5 30}} or cg_helix {{5 30} {35 65}}.
The first two results in a long ribbon or some weird shape that includes both peptides and the last give me a not a valid argument" error.

As I said I think the problem is that I have two peptides, both having residues numbered from 1 to 33. It works with a gro file containing only 1 peptide. Is there a way to specify it, something like -segname?

Thank you,
Giota

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