Greetings. I have already posted a similar question on the forum previously and hence i am writing to your email. My problem is when i open a protein pdb, i get wonderful ribbon representation when i opt for it. But when i give a protein pdb with only a CA atoms/ CA,C,N atoms, i dnt get the ribbon representation. I understand that ribbon is constructed by considering CA,C,N,O and OXT atoms. What i did was that i simply removed O and OXT atoms by going through Tools--> Depiction --> Ribbon style Editor. It may be a wrong idea to do that. But i would appreciate if you could write me some way to draw the ribbon for protein having only CA or CA,C,N atoms IF POSSIBLE.
Regards, Bala
Hi Bala, If you have N-CA-C atoms, it actually works pretty well if you open Ribbon Style Editor, go to the "Residue Class" tab, choose "amino acid" but then change the "Orientation atom" to C instead of O, and Apply. (You still need to show ribbon if you didn't already do that.) You can save and name the new residue class for re-use in some later Chimera session if you want. The resulting ribbon looks the same to me as the standard ribbon made from N,CA,C,O (I tested this by writing a PDB of only the N,CA,C atoms from a complete structure, reading it back in, and experimenting with Ribbon Style Editor). http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbons... If you have CA atoms only, then there is no way to figure out the plane of the ribbon - it does not work to set both the "Guide atom" and "Orientation atom" to CA. Unfortunately this prevents you from displaying "licorice" ribbons even though they don't use an orientation plane. My only solution in this case is to use some program to build the additional atoms from the CA trace, for example this web server: http://www.ebi.ac.uk/Tools/maxsprout/index.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html