Re: [Jmol-users] Can't open some XYZ files

[Miguel <mi...@jm...>]

> Hi there
>
> I've been using JMol

Please say =22Jmol=22 instead of =22JMol=22 ... lower case M

There is another project known as 'JMol'

> for about a year for visualising XYZ files and it
> works great but once in a while I come across a file I can't open. They=

> are usually rather big (>50,000 atoms) but some are actually a lot
> smaller (<5000 atoms). This is what the console says:
>
> <console>
> FileManager.openFile(C:=5CProgram Files=5CJMol=5Csb4394.xyz)
> SmarterJmolAdapter:The Resolver thinks:Xyz
> openFile(C:=5CProgram Files=5CJMol=5Csb4394.xyz) 141 ms
> Exception in thread =22Thread-6=22 java.lang.ArrayIndexOutOfBoundsExcep=
tion:
> 64

=5Bsnip=5D

> Does anyone have an idea?

This is a bug that has been fixed.

I do not recall all the details, but I believe it had to do with a
relatively large number of atoms with exactly the same coordinate value
along one or more dimensions.

> There is of course the possibility that
> these files are corrupt but all my XYZ files are created by the same
> programme and they usually work fine. Btw I'm using JMol 10.00 and Java=

> 1.5.0_04 on Windows XP.

This works in the 'prerelease' development version of Jmol. It can be
downloaded from

   www.jmol.org/files

> Here are two examples which don't work for me:
> http://www2.phys.canterbury.ac.nz/=7Emuk10/sb4394.xyz (180kB)
> http://www2.phys.canterbury.ac.nz/=7Emuk10/sb71104.xyz (3MB=21)

These files both work fine with Jmol Version 10.00.18

If you are regularly working with large files, you may want consider
compressing them with gzip. Jmol will automatically recoginze the fact
that they are compressed and will decompress them. File extension does no=
t
matter, so sb71104.xyz -> sb71104.xyz.gz is fine.



Miguel