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

[Gurudeeban Selvaraj]

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!
 
------------------
 Sincerely
 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  
ORCID:http://orcid.org/0000-0002-7223-3853

 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:

<http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>

Good luck,
Elaine
-----
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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