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Questions and answers => General discussions (Q&As) => Topic started by: ghzheng on September 21, 2007, 03:39:04 pm

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Title: Calculate step parameters given two planes
Post by: ghzheng on September 21, 2007, 03:39:04 pm

Hi,

Is there any function of X3DNA that can provide the 6 step parameters between two planes whose origins and orientations are given? For example, we can have a file including such information:

plane #   OX   OY   OZ    Xx   Xy  Xz  Yx  Yy  Yz  Zx  Zy  Zz
plane 1    *      *     *     *     *    *     *    *   *    *    *   *
plane 2    *     *      *     *     *    *     *    *   *    *    *   *

then, 3DNA can tell the step parameters.


Or shall we write own codes to do this, by following the technical algorithms in the 3DNA mannual?

Thanks.

Title:
Post by: xiangjun on September 22, 2007, 09:10:41 pm

Of course, such a function is implemented in the 3DNA source code. However, please see FAQ #3 (http://http://rutchem.rutgers.edu/~xiangjun/3DNA/faq.html#code).

There is no such a stand-alone program distributed with 3DNA. As you guessed, your best bet is to refer to the 3DNA user's manual (http://http://rutchem.rutgers.edu/~xiangjun/3DNA/manual/x3dna.pdf) for a detailed step-by-step example on how this is done in 3DNA. Following the procedure, it then should be a straightforward process to implement the algorithm in your favorite programming language.

HTH,

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