ERROR: plot.enma() example

[Barry Grant]

Running the example in plot.enma.Rd gives the error below.

Also, the internal call to dssp() could lead to an error if dssp is not available (or if a user has an old version - like I do on my laptop). Perhaps we can just proceed with a warning and without sse annotation if this happens?

> example(plot.enma)
Error in plot.window(xlim, ylim, ...) : need finite 'ylim' values

> plot.enma(all.modes, pdbs)
Hit <Return> to see next plot:
Error in plot.window(xlim, ylim, ...) : need finite 'ylim' values
In addition: Warning message:
In if (y == "deformations") yval <- x$deform else yval <- x$fluctuations :
  the condition has length > 1 and only the first element will be used
> plot.enma(all.modes, pdbs=pdbs)
Hit <Return> to see next plot:
Error in plot.window(xlim, ylim, ...) : need finite 'ylim' values

[Barry Grant]

I enclosed this example section in the Rd file with a donturn for now but the issue remains open.

[Lars Skjærven]

funny I haven't noticed this before. fixed now by including na.rm=TRUE when setting the ylim.

For the dssp - isnt this OK?

> plot.enma(all.modes, pdbs=pdbs)
Error in dssp(pdb.ref) : Launching external program 'DSSP' failed
  make sure 'dssp' is in your search path

[Barry Grant]

Will dssp errors such as this result in no plot being produced?

If so, why not just make the plot without dssp annotation - it should not be the limiting factor here in my view. By the way do you have a recent dssp build for mac. My build process is messed up with the update to OS X 10.9...

[Lars Skjærven]

Included a try() on the dssp() function call with some improved messaging.

> plot.enma(all.modes, pdbs=pdbs)
Warning message:
In plot.enma(all.modes, pdbs = pdbs) : SSE cannot be drawn
  Launching external program 'DSSP' failed

I only have OSX 10.8.5 at the moment.

[Barry Grant]

This new function version works well. thanks Lars!

[Barry Grant]

I am marking this as resolved.