Hi Yizhen, We try to show the data as described in the file and not guess whether it should be two -SH groups or one S-S because CYS is a standard residue (defined as -SH). The guessing based on radii and distance is normally used for nonstandard residues that do not have CONECT records. However, if you wish to add a bond there, you can. If there are hydrogens on the sulfurs you would need to delete those hydrogens first. In Chimera, you would need to select the two sulfur atoms and specify them by "sel" in the "bond" command: bond sel ... or instead of selecting, directly specify them by chain ID, residue number, and atom name. E.g. bond :33.A@sg :46.B@sg In ChimeraX instead of Chimera, just doing it for all cysteine SG pairs that are close together is much easier because it has a "reasonable" bond length option and you can create several bonds in a single command. For example, using an alphafold model which has several cysteine -SH pairs, you could use ChimeraX commands: open alphafold:LDLR_HUMAN color white label :cys show :cys color :cys byelement view :350-370 bond :cys@sg reasonable true I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 28, 2023, at 12:54 AM, Wang Yizhen via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear developers of UCSF chimera,
I am interested in the reason why chimera recognize the disulfide bond only by the CONNECT record in PDB files. Why not use the bond identification algorithm as used on other heavy atoms (sum of the covalent bond radii and tolerance 0.4A) to show the bond? Is there any special considerations for this?
Thanks in advance for any help.
Yizhen