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I am currently working on a project that requires X3DNA. The project is using programs such as VMD and RasMol to create duplexes of DNA strands; one which is phosphorous based and the other which is arsenic based. Once the structures are created they are then converted using OpenBabel from a .xyz file to a .pdb or vice versa. However, X3DNA is unable to run in the converted files. I was wondering if X3DNA was capable of converting the files itself, and if not would you be willing to point me in the direction of some other file converter that might work better.
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Others and I may help you better if you are specific about the DNA duplexes created with "VMD and RasMol", e.g., by attaching a sample file. Moreover, what format are those structures in initially? Is it PDB? If so, then why do you need to convert the files between .xyz and .pdb using OpenBabel?
By design, 3DNA only accepts compliant PDB format (http://www.wwpdb.org/docs.html), as documented clearly in the PDB website. Please see the following two blog posts for more details:
- PDB format, how many variants are there? (http://xiang-jun.blogspot.com/2010/08/pdb-format-how-many-variants-are-there.html)
- PDB ATOM coordinates record (http://xiang-jun.blogspot.com/2009/05/pdb-atom-coordinates-record.html)
HTH,
Xiang-Jun
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.
