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

Paris Tzou paristzou at gmail.com
Sun Nov 18 21:39:27 PST 2018

This is great, thank you so much!

Elaine Meng <meng at cgl.ucsf.edu> 於 2018年11月19日 週一 上午2:24寫道:

> 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:
> <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
> and/or
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/menutut.html>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.html
> >
> Also, this tutorial includes using FindHBond:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
> (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
> ~select
> 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:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>
> (2) As explained in the hbonds command help, you can remove hbonds, for
> example with command
> ~hbond
> (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:
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html
> >
> 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 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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