Bugs item #2986050, was opened at 2010-04-12 13:25
Message generated for change (Comment added) made by gutow
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Category: File Input/Output
Group: v11
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Miguel (migueljmol)
Summary: Cube file reading incorrect for large grid
Initial Comment:
Hi, I have a cube file that is relatively large:
N-methylacetamide potential
Electrostatic potential from Total SCF Density
12 -10.240476 -7.584863 -6.513163
101 0.200808 0.000000 0.000000
77 0.000000 0.200808 0.000000
66 0.000000 0.000000 0.200808
6 6.000000 3.423012 -1.072110 0.000161
6 6.000000 0.921643 0.333341 -0.000411
7 7.000000 -1.164821 -1.181425 -0.000117
and so on. When jmol reads the file the atoms are not displayed. If I change
the number of cells in the x-direction to 99 it works. The file reads correctly
into Avogadro if that is any help. It was generated by Gaussian 03. Tested with
jmol 11.8.15, 11.8.22, and 12.0.RC4.
The example file is too big to upload, but it is at my website here:
http://folding.bmc.uu.se/N-methylacetamide3.cub.gz
Thanks, David.
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Comment By: Jonathan Gutow (gutow)
Date: 2010-04-12 14:01
Message:
I don't think cube files contain any molecular information only. I suspect
you are loading the cube file on top of a molecule file in these other
applications. Try opening the gaussian file first and then loading the
cube file. You also might note that Jmol can make its own MEP on the total
electron density map from guassian files.
Jonathan
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