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

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:
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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 -0.2067It 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
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