rotate_mol rotfile.dat

[Marcp]

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 ...)

[xiangjun]

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

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   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.,

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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

[Marcp]

Thank you and good luck for 2.0