view.cnapath() shortest path color

[Former user]

Is there an option to change the color of the shortest path in .vmd file saved via view.cnapath?

[Xinqiu Yao]

We don't have options to adjust colors presently. The quickest way to achieve it is to modify the plot function a little bit and call it in an R session. For example, to display all paths as red

myfun <- edit(bio3d::view.cnapath)
# an editor will be invoked 
# change the line 'cols <- colorRampPalette(c("blue", "red"))(256)' to
# 'cols <- colorRampPalette(c("red", "red"))(256)'
# save the file and quit the editor

myfun(path, pdb, launch=TRUE)

You can do similar things for other colors.

Let me know if it works...

[Xinqiu Yao]

Hi,

A new option "colors" has been added to the function in the latest commit (commit).

For example,

# show all paths in red
view.cnapath(pa, pdb=pdb, colors="red", launch=TRUE)

# show paths from blue (longest) to green (shortest)
view.cnapath(pa, pdb, colors=c("blue", "green"), launch=TRUE)