Hi Ellie, I'm told that the "reasonable" option checks for distance, i.e. within the expected bond length plus a bit of tolerance. However, be aware that even if you get a bond with that option turned on, the bond could still be unreasonable for various other reasons, such as poor angles, some atom has too many atoms total bonded to it, etc. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds> For your specific question, your choices are any of the following: (1) turn off the "reasonable" option (2) move the glycan before using "combine" so that the two atoms to be bonded are closer together (3) instead of doing the positioning yourself and then using "combine" to merge the models, use the "Join Models" section of Build Structure and specify bond length and angles as needed in the "Other Bond" settings. That will move the separate glycan model to generate the specified length and angle, merge it into the protein model, and form the bond. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#join> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 14, 2024, at 12:28 PM, Eleanor Streeper via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Chimera X,
I hope you are well. I am a student at Swarthmore College and am currently trying to use Chimera X to covalently attach glycans to asparagine residues. I was able to get 3 out of 5 of the glycans attached by selecting both atoms > structure editing > build structure > adjust bonds > add reasonable bonds. I did the same process for the other 2 glycans and no bond was made. The log says bond sel, 0 bonds. The glycans are combined with the protein using the combine command.
I believed it may be an issue with an unreasonable binding distance but when I moved the glycan closer, the bond still didn't work. What else should I try? Also, do you know why it is working for some glycans but not others?
Best, Ellie Streeper