unanswered cg_helix for multiple proteins in vmd

  • tfischb
  • tfischb's Avatar Topic Author
  • Offline
  • Fresh Boarder
9 months 1 week ago #7782 by tfischb
cg_helix for multiple proteins in vmd was created by tfischb

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.

Part of the message is hidden for the guests. Please log in or register to see it.

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

Please Log in or Create an account to join the conversation.

Time to create page: 0.086 seconds