Bugs item #1598349, was opened at 2006-11-17 07:22 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1598349&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: File Input/Output Group: v10.9 >Status: Closed >Resolution: Wont Fix Priority: 5 Private: No Submitted By: Noel O\'Boyle (baoilleach) Assigned to: Miguel (migueljmol) Summary: Gaussian Cube File incorrect units Initial Comment: Hello Miguel, Bob, I am trying to visualise isosurfaces of cube files which I have generated myself. Jmol's cube file reader assumes that the cube file units are in Bohrs. However, this is only true if the 'number of points' is a negative value. Otherwise, the units are Angstroms (this applies to the units of the origin, as well as the units of the spacing). This is described briefly at http://local.wasp.uwa.edu.au/~pbourke/dataformats/cube/: """ If the sign of the number of voxels in a dimension is positive then the units are Angstroms, if negative then Bohr. """ I think the behavior is undefined if some of the signs of the 'number of voxels' are positive and some are negative (i.e. what units should be used for the origin in that case?). I would very much appreciate if you could fix this. Regards, Noel ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2006-11-30 14:37 Message: Logged In: YES user_id=1082841 Originator: NO Noel, Ah, yes. Quite a long history this issue has. I'm sorry, but that page you reference has an error. Somehow, somewhere along the way this specification was changed, and Gaussian Cube files -- despite the clear indication that only a negative count should indicate Bohr -- are all in Bohr, even with the count positive. Evidence of this is given in the code at http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c which reads the files as Bohr even with N > 0. I understand your pain. If you are trying to read the file just for its atom coordinates, you are out of luck; if you are reading the file specifically for its surface and you can get the coordinates from another file, try the "angstroms" isosurface option. Bob Hanson Bob ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1598349&group_id=23629 ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
