[Chimera-users] Doubt regarding the analysis of covalent bonds between the ligand and protein

[Elaine Meng]

Hi Krishna,
There is no option to identify covalent bonds if they are not already in your structure when you open it.  If you show all atoms (e.g. menu: Presets... Interactive 2 (all atoms), all the covalent bonds that are already in the structure, as defined in your input file(s), will be displayed.

It is impossible to tell whether the 0 H-bonds is an error or not without knowing your same exact structure and knowing all of the tool options or the exact command that you used.  Maybe there are really not any H-bonds between the protein and the ligand, or maybe the command or dialog options that you used were wrong.

If you are using the ViewDock tool, see the ViewDock tutorial that includes finding H-bonds:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html>

If you are not using ViewDock, maybe this other tutorial that includes finding H-bonds between the protein and ligand parts of a structure will be helpful:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 17, 2023, at 7:12 PM, Krishna Priya K R via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> I am a MSC student working on docking . By using UCSF chimera 1.14 I tried to analyse the H bonds and covalent bonds.
> 
> Even after following every step for H bond analysis it shows 0 bond and i am not able to find the option to analyse the covalent bond between the protein and ligand.
> 
> Hope you will help me to rectify my problem. 
> 
> My contact details : 8848890240
> Email id : krishnapriyaifs1999 at gmail.com