[Chimera-users] Query (how to find H-bonds)

Gurudeeban Selvaraj gurudeeb99 at qq.com
Sat Sep 30 19:38:27 PDT 2017

Dear Dr. Elaine

Thanks! But I want to see protein and ligand (peptide) structure. I could not see ligand, the display shows only protein structure. 
The file I enclosed is docked result. Instead of ligand there is a dotted line in between the protein.....I could not see this before.

The attachment file has (2 to 195 protein) and (1-7 peptide). I can see the individual structure in separate file but I could not see in same pdb file (docked result). 

The tutorial is not helping to fix the issue

Please make me clear!
 Dr. Gurudeeban Selvaraj, Ph.D.
Postdoctoral Researcher
Center for Food Science and Technology
School of Chemical Engineering and Environment 
 Henan University of Technology, Zhengzhou, China
 Mobile: +86 1883 800 2927; +91 84890 55578  

 Residence: Room No. 503, Foreign Teacher's Apartment, University Garden, Lianhua Street No. 50, Hi-Tech development Zone, Zhengzhou, 450001, China


------------------ Original ------------------
From:  "meng";<meng at cgl.ucsf.edu>;
Send time: Sunday, Oct 1, 2017 1:28 AM
To: "Gurudeeban Selvaraj"<gurudeeb99 at qq.com>; 
Cc: "UCSF Chimera Mailing List"<chimera-users at cgl.ucsf.edu>; 
Subject:  Re: [Chimera-users] Query (how to find H-bonds)

Dear Dr. Selvaraj,

Probably you just need to display the atoms, command “display” or menu: Actions… Atoms/Bonds… show.

This is just a general part of using Chimera.  I recommend going through the “Getting Started” tutorial to become more familiar with the program:


Good luck,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 30, 2017, at 4:57 AM, Gurudeeban Selvaraj <gurudeeb99 at qq.com> wrote:
> Dear Dr.Elaine,
>           Thanks for the information. It is working now but some of them I could not see hydrogen bonds (Intra). Now I could not see the ligand structure of the docked result in Chimera.
> I have enclosed file and snap shot of my issue. Let me know, what will do?
> <3_8_sol_3.ref.pdb><image.jpg>
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