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VMD scripting

Tips

Show the list of available render commands

render list

Delete graphics

graphics top delete all

Drawing arrows

arrow1/

A simple TCL script to draw arrows.

$ vmd 2igd.pdb
[Tk console]$ source vector1.tcl

arrow2/

In case there are many arrows to be drawn (such as results of Nomal Mode Analysis and Principal Component Analysis), a python script pca_tcl_arrow.py can be used to generate a TCL script file.

$ ./pca_tcl_arrow.py  template.tcl  ev1.vector  1  227  ev1.tcl
$ vmd -e trna.vmd
[Tk console]$ source ev1.tcl

In this example, vector data for 227 points is stored in ev1.vector in order like {x1, y1, z1, x2, y2, z2 ...., x227, y227, z227}.

Special thanks to Mr. Fuyuki Sakai

Credit and Disclaimer

Some of scripts here were adopted and modified from the script library in the official VMD website. https://www.ks.uiuc.edu/Research/vmd/script_library/ , thus all follow the original redistribution policy quoted below.

VMD script library redistribution policy Scripts in the library are freely available for anyone to use and modify but may not be sold. They are distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Should the software > prove defective YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.