[Chimera-users] Chimera using problem

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 11 10:12:27 PDT 2016

Hi Chonghua Ren,
If you already know the 4-digit identifier for the Protein DataBank (PDB)  like 1d86, you can just use

(A) command: open 1d86
- OR -
(B) menu: File… Fetch by ID, and then for database “PDB” enter ID 1d86, click Fetch button at the bottom

This just gets the structure from the PDB database.  It does not use the sequences of the molecules in the structure.

How you could look at interactions between DNA and protein is the same as for between any two molecules (protein-protein, protein-small molecule etc.).  Some of the tools that might be useful:

(1) FindHBond (or command “findhbond”)
(2) Find Clashes/Contacts (or command “findclash”)
(3) Coulombic Surface Coloring (or command “coulombic”)
(4) Distances (or command “distance”)

The graphical interfaces of these tools are in the menu under Tools… Structure Analysis and/or Surface/Binding Analysis.  You can click the Help button on each tool dialog to see its manual page, or use “help command-name” to see the command help (for example, command: help findhbond) and there are also tutorials:


I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 11, 2016, at 2:20 AM, Chonghua Ren <chren at ucdavis.edu> wrote:
> Dear there,
> I am learning how to use Chimera now, I like it so much and find it is so awesome. I have one question, if I want to input a DNA sequence like ID "1d86", how can I transfer the DNA sequence to PDB format? Another question, how can I know protein and DNA interaction using this software?
> Thank you so much!
> Best wishes,
> Chonghua Ren

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