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General discussions (Q&As) / Re: Analyzing a PDB containing isolated bases
« on: November 15, 2006, 11:35:47 pm »
Dear Claudio,
Thanks for using 3DNA and your nice words about our work. Actually, as I mentioned in previously replies in this forum, it is the 3DNA users that are driving the further refinement and development of the package. Every user's question provide us a new prospective and opportunity to "Kaizen" (improve/refine) it.
Now back to your question, it is okay to run 3DNA on a nucleic acid structure without backbone atoms. The program "find_pair" will find the pairs and "analyze" will provide a detailed output of strucural parameters. Please have a look of the user's manual. The files "bp_step.par" and "bp_helical.par" are mainly for rebuilding purpose.
It will take time to get familiar with 3DNA and to use it more efficiently. If you have any further questions, please come back to this forum. In case you have some specific problems, you can attach your files and we will look into them.
HTH,
Xiang-Jun
Thanks for using 3DNA and your nice words about our work. Actually, as I mentioned in previously replies in this forum, it is the 3DNA users that are driving the further refinement and development of the package. Every user's question provide us a new prospective and opportunity to "Kaizen" (improve/refine) it.
Now back to your question, it is okay to run 3DNA on a nucleic acid structure without backbone atoms. The program "find_pair" will find the pairs and "analyze" will provide a detailed output of strucural parameters. Please have a look of the user's manual. The files "bp_step.par" and "bp_helical.par" are mainly for rebuilding purpose.
It will take time to get familiar with 3DNA and to use it more efficiently. If you have any further questions, please come back to this forum. In case you have some specific problems, you can attach your files and we will look into them.
HTH,
Xiang-Jun