From: <nve...@cl...> - 2005-08-29 08:13:13
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A: jmol-users=40lists.sourceforge.net > >Is ver 10 of jmol available for WinXP Pro? If so where? If not what ver i= s? = >And, where can I dwnld that ver? Jmol v10 is available for all platforms with Java 1.4 (maybe with older ve= rsions). You can download it from the main page http://sourceforge.net/projects/jmol/ Nicolas |
From: Angel H. <ang...@ua...> - 2005-11-19 12:59:34
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Hello, Aaron From ypur description, I think that your problem is not in Jmol, but in your drawing program being a 2D design, although it saves in MOL format it is still 2D. You need a program that will generate / optimize / minimize your structure into 3D, then you can save in MOL format. I can suggest ACD Labs' ChemSketch Freeware. It allows you to draw (possibly to import your existing MOL files), then to 3D-optimize, then to save as MOL. |
From: Jonathan G. <gu...@uw...> - 2021-01-13 18:03:44
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> Jonathan, take a look through the code at SourceForge on line and tell me > where this is located and what you want changed. > Bob Removing line 180 of script_btn_template.html in webexport/html, will remove the link and text providing the option to use Java. Thanks, Jonathan Dr. Jonathan Gutow Chemistry Department UW Oshkosh web: https://uwosh.edu/facstaff/gutow e-mail: gu...@uw... Ph: 920-424-1326 |
From: <dr...@ma...> - 2005-11-19 15:27:26
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Hi, I don't think jchempaint can generate 3D coordinates, perhaps the easiest way to convert them is to use CORINA (http://www2.ccc.uni-erlangen.de/software/corina/ free_struct.html) which gives free access for 1000 structures. It just requires a SMILES string as input. You might also be interested in iBabel for viewing structures (http://www.macinchem.fsnet.co.uk/applescripts.htm) Chris > Message Received: Nov 19 2005, 07:30 AM > From: "Aaron Glimme" <ag...@ca...> > To: jch...@li..., jmo...@li... > Cc: > Subject: [Jchempaint-user] (no subject) > > I've been using jchempaint for a while to draw structures for my > chemistry tests, now I need to turn some of them in to 3d models and > I'm having some trouble. I've tried saving the file as a MDL MOL file > and CML files and then opening it in Jmol. There are two issues with > this that I haven't been able to figure out. > > The first is the bond length seems really large in Jmol I'm having > trouble getting the files to look like a ball and stick model. The > second is the geometry isn't working, the models come out in a 2d > plane, is there some trick or script I need to run to get the > geometry right. I haven't been able to figure it out yet, any help > would be much appreciated. > > I'm using the latest versions of all the apps in Mac OS X 1.4.3. > > > Aaron Glimme > Berkeley High School > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > Register for a JBoss Training Course. Free Certification Exam > for All Training Attendees Through End of 2005. For more info visit: > http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click > _______________________________________________ > Jchempaint-user mailing list > Jch...@li... > https://lists.sourceforge.net/lists/listinfo/jchempaint-user > > |
From: Christoph S. <c.s...@un...> - 2005-11-20 20:54:02
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We have recently been releasing a 3D coordinate generator for the CDK, wh= ich is=20 available for testing at http://www.chemistry-development-kit.org. There, you can draw a 2D structure in JChemPaint and have it converted in= to a 3D=20 structure. It would not be much effort to include it into JChemPaint. Be aware, however, that it is by no means as sophisticated as CORINA, and= may=20 fail on structures where it cannot find the right ring coordinates (which= it=20 takes from template in an internal database). Cheers, Chris dr...@ma... wrote: > Hi, >=20 > I don't think jchempaint can generate 3D coordinates, perhaps the easie= st way to convert them is to use CORINA (http://www2.ccc.uni-erlangen.de/= software/corina/ > free_struct.html) which gives free access for 1000 structures. It just = requires a SMILES string as input. >=20 > You might also be interested in iBabel for viewing structures (http://w= ww.macinchem.fsnet.co.uk/applescripts.htm) >=20 > Chris >=20 >=20 >=20 >>Message Received: Nov 19 2005, 07:30 AM >>From: "Aaron Glimme" <ag...@ca...> >>To: jch...@li..., jmo...@li...urceforge= .net >>Cc:=20 >>Subject: [Jchempaint-user] (no subject) >> >>I've been using jchempaint for a while to draw structures for my =20 >>chemistry tests, now I need to turn some of them in to 3d models and =20 >>I'm having some trouble. I've tried saving the file as a MDL MOL file =20 >>and CML files and then opening it in Jmol. There are two issues with =20 >>this that I haven't been able to figure out. >> >>The first is the bond length seems really large in Jmol I'm having =20 >>trouble getting the files to look like a ball and stick model. The =20 >>second is the geometry isn't working, the models come out in a 2d =20 >>plane, is there some trick or script I need to run to get the =20 >>geometry right. I haven't been able to figure it out yet, any help =20 >>would be much appreciated. >> >>I'm using the latest versions of all the apps in Mac OS X 1.4.3. >> >> >>Aaron Glimme >>Berkeley High School >> >> >>------------------------------------------------------- >>This SF.Net email is sponsored by the JBoss Inc. Get Certified Today >>Register for a JBoss Training Course. Free Certification Exam >>for All Training Attendees Through End of 2005. For more info visit: >>http://ads.osdn.com/?ad_id=3D7628&alloc_id=3D16845&op=3Dclick >>_______________________________________________ >>Jchempaint-user mailing list >>Jch...@li... >>https://lists.sourceforge.net/lists/listinfo/jchempaint-user >> >> >=20 > =20 >=20 >=20 >=20 > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > Register for a JBoss Training Course. Free Certification Exam > for All Training Attendees Through End of 2005. For more info visit: > http://ads.osdn.com/?ad_id=3D7628&alloc_id=3D16845&op=3Dclick > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users >=20 >=20 >=20 --=20 Priv. Doz. Dr. Christoph Steinbeck (c.s...@un...) Head of the Research Group for Molecular Informatics Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.d= e) Z=C3=BClpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: Jonathan G. <gu...@uw...> - 2021-01-13 17:43:08
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Sorry about the previous e-mail to the list without a subject line. > Jonathan, take a look through the code at SourceForge on line and tell me > where this is located and what you want changed. > Bob Removing line 180 of script_btn_template.html in webexport/html, will remove the link and text providing the option to use Java. Thanks, Jonathan Dr. Jonathan Gutow Chemistry Department UW Oshkosh web: https://uwosh.edu/facstaff/gutow e-mail: gu...@uw... Ph: 920-424-1326 ________________________________ From: Jonathan Gutow Sent: Wednesday, January 13, 2021 8:27 AM To: jmo...@li... <jmo...@li...> Subject: Re: > Jonathan, take a look through the code at SourceForge on line and tell me > where this is located and what you want changed. > Bob Removing line 180 of script_btn_template.html in webexport/html, will remove the link and text providing the option to use Java. Thanks, Jonathan Dr. Jonathan Gutow Chemistry Department UW Oshkosh web: https://uwosh.edu/facstaff/gutow e-mail: gu...@uw... Ph: 920-424-1326 |
From: Robert H. <ha...@st...> - 2021-01-14 03:36:25
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Jonathan, this is in https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.31/Jmol%2014.31.24/, though I forgot to mention that in Jmol.properties. On Wed, Jan 13, 2021 at 12:03 PM Jonathan Gutow <gu...@uw...> wrote: > > Jonathan, take a look through the code at SourceForge on line and tell me > > where this is located and what you want changed. > > Bob > > Removing line 180 of script_btn_template.html in webexport/html, will > remove the link and text providing the option to use Java. > > Thanks, > Jonathan > Dr. Jonathan Gutow > Chemistry Department > UW Oshkosh > web: https://uwosh.edu/facstaff/gutow > e-mail: gu...@uw... > Ph: 920-424-1326 > > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place.* |