[Jalview-discuss] trouble with Jmol

Jim Procter jprocter at compbio.dundee.ac.uk
Fri Jun 3 01:35:25 BST 2011

Hello Steven, sorry to hear you are having problems.

On 03/06/2011 07:54, Steven Adamson wrote:
> I'm a new Jalview user.  The program worked in its entirety at first, 
> but Jmol has ceased working.  A red line of text in the Jmol window reads:
>  java.io.FileNotFoundException: C\Program 
> Files\DOCUME~1serLOCALS~1Tempjalview_pdb64970.txt (The system cannotb 
> find the file specified)
To work out what's wrong, I need a little more information. When do you 
observe this message ?  Is it when the program first loads, and opens 
it's example alignment - or when you load in your own jalview project ?

Also, could you let me know what machine and java version you have, and 
send me any output on the Jalview console when this error occurs ?  To 
do this, first make sure that the Jalview Java console is enabled in the 
'Tools' menu of the Jalview desktop window. Then - close and restart 
Jalview, and once the error has occured in Jmol's window, copy and paste 
the contents of the text window into a file and send it to me as an 

I'm currently on holiday - but if you send me the console log, then I'll 
try and take a quick look to see if there's a simple workaround for your 


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