[Chimera-users] how to make/delete hydrogen bond and delete chains

Elaine Meng meng at cgl.ucsf.edu
Sun Nov 18 10:24:44 PST 2018

Hi Paris,
You can do all of these things quite simply, it is just a matter of learning how to interact with Chimera.  See the “Getting Started”  tutorials for learning basic interactions with Chimera:

Also, this tutorial includes using FindHBond:

(1) You do not have to make the two parts for hbond as two separate models: you can specify any 2 sets of atoms even if they are in the same model.  If you are using the “hbond” (findhbond) command, this is done by selecting some of the atoms and using the “selRestrict” option, for example commands:

select nucleic acid
hbond  selRestrict protein reveal true

The FindHBond dialog also has options to do this. Click the Help button on the dialog or use command “help hbonds” to see the help because there are lots of other options you could also use at the same time. There are several different ways to select, as explained here:

(2) As explained in the hbonds command help, you can remove hbonds, for example with command


(3) You must be specifying the chain incorrectly.  For example this deletes chain B:

delete :.B

(or if you find it difficult to use commands, you can select the chain with the Select menu and delete it with the menu Actions… Atoms/bonds… delete).  Command-line specification is explained here:

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

> On Nov 17, 2018, at 5:43 PM, Paris Tzou <paristzou at gmail.com> wrote:
> Hi,
>    I have a protein-dna complex structure with protomer as A as protein and B as DNA. It is impossible in hbond function to "generate" hbonds between two chains (A and B). One have to parse protein and DNA into two files and load into Chimera as two models. Another question is that, once generated, hbonds cannot be "erased" in the chimera view. And "delete chain ID" cannot really delete one chain from protein-DNA complex. What I am doing is 5MCT, p53-DNA complex.
> Thanks a lot for your help.
> Paris

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