pcavec_drawer
This tool generates VMD and PyMol files to visualize PCA vectors. The parameters in [OPTION] specify length, size, and color of vectors drawn in VMD and PyMol.
[INPUT] pdb_avefile = ../1_avecrd/output_ave.pdb # PDB file obtained by avecrd_analysis vecfile = ../3_eigmat/output.vec # VEC file obtained by eigmat_analysis [OUTPUT] vmdfile = output.vmd # VMD visualization state file pmlfile = output.pml # PyMol script file [OPTION] check_only = NO # (YES/NO) mode_no = 1 # PCA mode number to be visualized expand_vector = 25.0 arrow_length = 1.5 cylinder_radius = 0.15 cone_radius = 0.45 arrow_reverse = NO # reverse the arrow direction vector_color_vmd = yellow # color name for [VMD] vector_color_pml = 0, 1, 1 # RGB color (0.0-1.0) for [PyMOL]
For VMD, run the following command:
$ vmd ../1_avecrd/output_ave.pdb -e output.vmd
For PyMol, run the following command:
$ pymol output.pml
PyMOL> set ribbon_sampling, 1
PyMOL> set ribbon_trace, 1
PyMOL> set ribbon_width, 8
PyMOL> show ribbon, output_ave
