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Questions and answers => General discussions (Q&As) => Topic started by: lrush88 on July 08, 2009, 11:06:55 pm

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Title: DNA Rotation
Post by: lrush88 on July 08, 2009, 11:06:55 pm

Dr. Xiang-Jun Lu,

I am running MD simulations with DNA, and I am using your program to calculate the deformation energy and to generate quality images from applied motions. I am having problems with the images that are generated, because they are rotating after some of the runs so I cannot see exactly what is happening to the DNA molecule.

                                                                    Thank you,
                                                                    L. E. Rush Jr.

Title: Re: DNA Rotation
Post by: xiangjun on July 08, 2009, 11:50:47 pm

Thanks for using 3DNA. I am glad that you are taking advantage the visualization part of 3DNA: the other day, I blogged on blocview (http://http://xiang-jun.blogspot.com/2009/06/blocview-simple-effective-visualization.html) wondering why it has not been used that much.

Could you be more specific? Which command and options did you use? Preferably with a reproducible example?

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University