[Chimera-users] Information regarding double bonds

[Naima syed]

 Actually, I checked from 2 other softwares and when I checked via maestro it should they have hydrogen instead of double bond which initially was not present in my docked file
    On Monday, November 14, 2022 at 04:15:10 PM EST, Elaine Meng <meng at cgl.ucsf.edu> wrote:  
 
 How do you know it was lost?  Is it from the number of hydrogens added by dock prep? 
Elaine


> On Nov 14, 2022, at 1:10 PM, Naima syed via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello, 
> 
> Yes, but my question is that I know I have a double bond and I confirmed this double bond from PyMol software but after docking this was removed. Can you please tell me the reason. Actually when I just do dock prep, double bond was lost.
> 
> On Monday, November 14, 2022 at 04:04:35 PM EST, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 
> Hi Naima,
> Chimera does not display double bonds with two lines, if that is what you mean.  I.e. it will be shown with one line or stick, but that does not mean it is a single bond unless you can somehow tell from other information such as number of added hydrogens.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                      
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> > On Nov 14, 2022, at 12:30 PM, Naima syed via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> > 
> > Hello,
> > 
> > I have one concern, before docking there is a double bond which i can check in pymol but after docking that double bond was lost. Can you please tell me how to fix this problem. 
> > 
> > Thank you
> 
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