unanswered cg_helix for multiple proteins in vmd

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9 months 1 week ago #7782 by tfischb
cg_helix for multiple proteins in vmd was created by tfischb
Hello,

for my Bachelor thesis I am trying to visualize the secondary structure of a system that consists of multiple proteins. In order to achieve this goal cg_helix and vmd is used. Please receive all the Files I'am talking about in the link below.


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For Illustration purposes I made an minimal System.
For a single protein cg_helix works fine (see single.pdb and single.dat) but as soon as there are multiple proteins things are getting weird. For two proteins only a single helix is drawn and for 3 cg_helix draw messy lines.

To solve this I took different approaches:

- I played with the presence of termini in the ssdump file and pdb structure
- I made the residues continuous in the pdb structure
- I selected the proteins manual via tk in vmd but I found no way that cg_helix uses the selected residues.

Also I tried to enter the position of the helices manually, but as soon as the second protein is reached I got a range error.

Every help is appreciated.

Thank you and kind regards,
Tobias Fischbach

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