ERROR: plot.enma() example
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
Comments (6)
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reporter -
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
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reporter 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...
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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.
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reporter This new function version works well. thanks Lars!
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reporter - changed status to resolved
I am marking this as resolved.
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I enclosed this example section in the Rd file with a donturn for now but the issue remains open.