[Chimera-users] Adding residue to two sides of DNA

Eric Pettersen pett at cgl.ucsf.edu
Mon Jun 16 16:37:21 PDT 2014

Hi Mahdi,
	Here's something that may or may not get you a useable structure:

1) Use Build Structure to create a model DNA that includes the sequence of your existing DNA in its middle, with the additional three base pairs on each end.
2) Superimpose your model on the middle of the model DNA ("match" command)
3) Delete the middle of the model DNA ("delete" command, possibly by using the Sequence tool to select the appropriate residues and then "delete sel")
4) Combine your DNA with the remnants of the model DNA into one model ("combine" command)
5) Add the connecting bonds between the fragments (select each atom pair and "bond sel")
6) Minimize the result, possibly only allowing the model portion to move ("minimize" command)


                        Eric Pettersen
                        UCSF Computer Graphics Lab

On Jun 16, 2014, at 4:24 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Mahdi,
> Sorry, Chimera only includes changing the type of a nucleotide that is already in the DNA structure (command "swapna"),
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html>
> ... or building a whole double helix from scratch, that is, without any starting structure (menu: Tools… Structure Editing… Build Structure, section: Start Structure, option: helical DNA/RNA)
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start>
> I don't have much experience building DNA.  Here are a couple web-servers, but I think they also only build entire structures from scratch:
> <http://structure.usc.edu/make-na/>
> <http://w3dna.rutgers.edu/index.php/rebuild>
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Jun 16, 2014, at 3:53 AM, Mehdi Bagherpour <mehdi.bpour at gmail.com> wrote:
>> Dear Chimera Users,
>> I want to add 3 base-pairs to two side of DNA.
>> I tried more about that but I couldn't.
>> Could some one any idea about doing that in chimera or another programs.
>> Best Regards,
>> Mahdi
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