[Chimera-users] To build ssDNA to base pair with the other strand of DNA

Wei Shi wei.shi118 at gmail.com
Tue Jun 4 12:43:13 PDT 2013

Thank you so much for the suggestions! I got the suggestions from Edwin
Pozharski in ccp4bb and ended up using the Calculate->Other modeling
tools-> Base pair function in coot.  Thank you!


On Wed, May 29, 2013 at 2:01 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Wei,
> Sorry, (without having searched extensively) I don't know of any program
> that takes one DNA strand as input and builds just the complementary
> strand. There are certainly programs that build idealized DNA double
> helices, e.g. NAB and the make-na server:
> <http://structure.usc.edu/make-na/server.html>
> In Chimera, you can build a crude DNA double helix with the "rna" command
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html>
> ... and there is a very nice Chimera plugin called "Assemble2" for
> interactively designing RNAs in 2D and building/refining them in 3D
> <http://bioinformatics.org/assemble/index.html>
> ... but I realize these are not quite what you seek. Maybe you could try
> asking on the Comp Chem List (ccl.net) or the PDB list (pdb-l, see
> https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l)
> Best,
> 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 May 29, 2013, at 10:36 AM, Wei Shi wrote:
> > Hi all,
> > I am working on solving the crystal structure of a protein-DNA complex.
> I could complete one strand of the DNA to fit the electron density using
> Coot, but for the other strand, the density for several bases at each end
> of the DNA is not clear and it's missing several bases at each end of the
> DNA. I am wondering whether in chimera, there is a function I could use to
> build the missing bases in one strand of the DNA to base pair with the
> other strand of DNA which is complete. Thank you so much!
> > Best,
> > Wei
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