From: Robert H. <ha...@st...> - 2009-04-06 15:40:59
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I'll need to see those files. I suspect something is happening to the 2d mol file when you are processing it; I'm not seeing the same problem with NIST data. For example, I take the 2d file for cholesterol, put it in a zip file, load the zip file, and it all works fine.... Bob On Sun, Apr 5, 2009 at 9:02 PM, John Shepardson <j.s...@co...>wrote: > I hope this isn't a double post, first tried from Nabble, unsuccessfully. > > > > I have been had a problem with molecules being drawn incorrectly when the > .mol file is in a zipped archive. > > The bonds just go all over the place and come out completely wrong. Big > molecules become a huge flat mess! > > > > This does not happen in 3d .mol files in zipped archives, only 2d. > > > > For instance Benzene from the NIST site (listed below) always comes out > with the bonds incorrectly drawn if it is in a zip file. All I do that > causes this bug is to put the .mol file into a zipped archive like "M2.zip" > in the project, and I use the jmol load like "load M2.zip|71-43-2-2d.mol" > > > > It loads and draws but the bonds are incorrectly drawn. > > If I take the file out and put it in the project folder and use "load > 71-43-2-2d.mol", all of the bonds are drawn correctly. > > > > Can anyone help me with this? One other thing, the 3d files often show an > incorrect Oxygen double bond that is pretty ugly, but not as bad as the > massive mistakes in the 2d files. > > Thanks > > John > > > > > > 1 "Benzene", ID: C71432 > > NIST 09040214522D 1 1.00000 0.00000 > > > > 6 6 0 0 0 1 V2000 > > 0.5047 1.7158 0.0000 C 0 0 0 0 0 0 0 0 0 > > 1.5140 1.7158 0.0000 C 0 0 0 0 0 0 0 0 0 > > 0.0000 0.8579 0.0000 C 0 0 0 0 0 0 0 0 0 > > 2.0186 0.8579 0.0000 C 0 0 0 0 0 0 0 0 0 > > 1.5140 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 > > 0.5047 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 > > 2 1 2 0 0 0 > > 1 3 1 0 0 0 > > 4 2 1 0 0 0 > > 3 6 2 0 0 0 > > 5 4 2 0 0 0 > > 6 5 1 0 0 0 > > M END > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Robert H. <ha...@st...> - 2009-04-07 20:03:32
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that's not acceptable --- please send the file so I can address this bug. On Mon, Apr 6, 2009 at 6:55 PM, John Shepardson <j.s...@co...>wrote: > >Date: Mon, 06 Apr 2009 12:29:00 +0200 > > >From: " Angel Herr?ez " <ang...@ua...> > > >Subject: Re: [Jmol-developers] Incorrectly Drawn Bonds in Zipped > 2d.mol files > > > > > This seems to be due to Jmol autobonding being applied in zipped files. > If I issue set autobond off > > > before loading the zip file, then it renders correctly. > > > > Thank you Angel, set autobond off fixed it. > > > > John > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > High Quality Requirements in a Collaborative Environment. > Download a free trial of Rational Requirements Composer Now! > http://p.sf.net/sfu/www-ibm-com > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: A. H. <ang...@ua...> - 2009-04-14 07:15:44
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I think it happens for 2D mol files that have funny bond distances. If the file is 3D (and so has proper bond lengths) or it is 2D with reasonable bond lengths, no problem. But when the file is 2D and has too short bond lengths (some programs do this, considering that a 2D structural formula does not follow angstrom lengths for bonds, so use arbitrary length units), Jmol is taking the declared bonds and adding its own autocalculated bonds. I will send some examples separately. And, as I said, issuing "set autobond off" prevents the problem. |