Using pymol to visualize cyclic peptide.
The cartoon representation of cyclic peptide is missing at the head to tail linkage which when represented with line and stick representation is complete.
Any suggestion to visualize the cartoon representation of cyclic peptide in pymol will be really helpful.
Have you tried to draw the structure in a structure-drawing program (for example Biovia Draw https://discover.3ds.com/biovia-draw-academic or ACDLabs https://www.acdlabs.com/resources/freeware/index.php are commercial but offer free versions for personal and academic use, Chemdraw https://perkinelmerinformatics.com/products/research/chemdraw/ is commercial) and export the result to pymol?
The problem is that the cartoon-generating algorithm does only look forwards in the chain for the next bond, and does not check whether the last amino acid in the chain could bond back to the first one. I am not aware of any structure viewer who does so.
If you just want to trick PyMol into showing a continuous ribbon: Copy a second instance of the coordinates of the peptide to the end of the peptide, renumbering the second copy accordingly (residues 1 to n) for the first and (n+1 to 2n) for the second instance. This will give you a continuous cartoon over the break since this is now within the chain, and you can undisplay whichever parts of the cartoon that do not look right.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools