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Topics - heldenbr

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Hello Dr. Lu and other users,

I am a very new user of 3DNA.  I have done some simulations of RNA and have found some examples of interesting base pairs in them.  Now I would like to search the PDB for other examples of these types of base pairs.  3DNA looks like it could be a very useful tool to accomplish this.

Like the user in this post: http://forum.x3dna.org/general-discussions/analyzing-a-pdb-containing-isolated-bases/msg35/#msg35 I have used Gaussian to optimize the gas phase structure of my base pair.  I have replaced everything beyond the glycosidic bond with a methyl group.  I have tried both Gaussview and OpenBabel to get my Gaussian output file into pdb format.  Some information is missing since Gaussian does not know/care about residue type, etc.  I have tried to add some of this information/reformat by hand, but I still worry that I do not have a correctly formatted file.

When I run find_pair with the options -pz on my pdb file, it does not find any pairs.  I suspect this is a formatting issue, although I do not hear any complaints from find_pair about missing fields (as I did when trying to run find_pair on the pdb file produced by Gaussview).

So I guess I have two questions:

1. Is the attached file properly formatted for use with 3DNA?

2. If find_pair does not find a base pair, will it still output the base pair geometry parameters that were calculated?  This would be very useful to me, because I believe that some of the base pairs I would like to search for may be outside of the default parameters.  This would tell me automatically how I should change 3DNA's base pair parameters to search the pdb for other examples.

Thanks!
-Hugh Heldenbrand
Graduate Student, U of MN

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.