To build ssDNA to base pair with the other strand of DNA
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
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
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! Best, Wei On Wed, May 29, 2013 at 2:01 PM, Elaine Meng <meng@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
participants (2)
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Elaine Meng -
Wei Shi