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Questions and answers => General discussions (Q&As) => Topic started by: Marcp on June 10, 2008, 05:13:07 am

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Title: rotate_mol rotfile.dat
Post by: Marcp on June 10, 2008, 05:13:07 am

Hello,

The rotate_mol program can take as input a data file containing a Transformation Matrix (rotmat.dat in the help displayed on screen), but what is the standard of this particular file ? (What is the size of the matrix, etc ...)

Title: Re: rotate_mol rotfile.dat
Post by: xiangjun on June 11, 2008, 07:47:19 pm

The format of the transformation matrix expected by 'rotate_mol' should be as follow:

Code: [Select]

   1  # x-, y-, z-axes row-rise
      0.0000      0.0000      0.0000
      0.3654     -0.9308      0.0000
     -0.1924     -0.0755     -0.9784
      0.9107      0.3575     -0.2067
It needs to be fed with option "-t=rotmat.dat": there is a typo in the help message, which has been fixed in v2.0. i.e.,

Code: [Select]

rotate_mol -t=rotmat.dat sample.pdb sample_rmat.pdbIn the coming 3DNA Nature Protocols paper, we have a concrete example of this functionality used to set an DNA-RNA junction structure with one helix region along x-axis, another (decomposed orthogonal component) along y-axis.

HTH,

Xiang-Jun

Title: Re: rotate_mol rotfile.dat
Post by: Marcp on June 13, 2008, 04:12:26 am

Thank you and good luck for 2.0

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