Thanks, Angel. I checked over the alignment of the pdb data and, though there wasn't anything obviously wrong, deleting some unnecessary data solved the problem.
I wonder why Jmol 11.2 was happy with the data as it was, but Jmol 11.4 and 11.6 didn't like it? Thanks again Ewen -----Original Message----- From: [email protected] [mailto:[email protected]] Sent: 13 February 2009 16:20 To: [email protected] Subject: Jmol-users Digest, Vol 33, Issue 19 Send Jmol-users mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/jmol-users or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of Jmol-users digest..." Today's Topics: 1. Re: script [file-name] LINE n (Robert Hanson) 2. Mac OS X (Amal CHLYEH) 3. Re: Mac OS X (Egon Willighagen) 4. Re: Bonds not showing in Jmol 11.6 (Angel Herraez) 5. Re: Mac OS X (Amal CHLYEH) 6. Re: Mac OS X (Angel Herraez) 7. Re: Mac OS X (Rolf Huehne) 8. Re: Mac OS X (Egon Willighagen) 9. Re: Mac OS X (Paul Pillot) ---------------------------------------------------------------------- Message: 1 Date: Fri, 13 Feb 2009 08:11:13 -0600 From: Robert Hanson <[email protected]> Subject: Re: [Jmol-users] script [file-name] LINE n To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset="iso-8859-1" script "myfile.spt" LINES 1 - 100 On Fri, Feb 13, 2009 at 6:02 AM, Jan H. Jensen <[email protected]> wrote: > script [file-name] LINE n seems to only execute line n, rather than > starting the script at line n. Is there a way to invoke the latter? > > Best regards, Jan > -- > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > Jan H. Jensen Associate Research Professor > Department of Chemistry [email protected] > University of Copenhagen Phone: +45 35 32 02 39 > Universitetsparken 5 FAX: +45 35 32 02 14 > 2100 Copenhagen Denmark > http://propka.ki.ku.dk/~jhjensen <http://propka.ki.ku.dk/%7Ejhjensen> > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > > > ------------------------------------------------------------------------ ------ > Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, > CA > -OSBC tackles the biggest issue in open source: Open Sourcing the > Enterprise > -Strategies to boost innovation and cut costs with open source > participation > -Receive a $600 discount off the registration fee with the source code: > SFAD > http://p.sf.net/sfu/XcvMzF8H > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- 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 -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ Message: 2 Date: Fri, 13 Feb 2009 14:03:24 +0100 From: Amal CHLYEH <[email protected]> Subject: [Jmol-users] Mac OS X To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Bonjour, je voudrais utiliser un ligiciel de visualisation des mol?cules en 3D mais je ne trouve rien qui puisse aller avec Mac OS X. Pouvez vous m'indiquer un site o? je pourrai trouver cela ? D'avance merci Pr. Amal CHLYEH Universit? Cadi Ayyad Facult? des Sciences Marrakech MAROC -- Ce message a ?t? v?rifi? par MailScanner pour des virus ou des polluriels et rien de suspect n'a ?t? trouv?. MailScanner remercie transtec pour son soutien. ------------------------------ Message: 3 Date: Fri, 13 Feb 2009 15:30:17 +0100 From: Egon Willighagen <[email protected]> Subject: Re: [Jmol-users] Mac OS X To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1 Hi Amal, 2009/2/13 Amal CHLYEH <[email protected]>: > je voudrais utiliser un ligiciel de visualisation des mol?cules en 3D > mais je ne trouve rien qui puisse aller avec Mac OS X. > Pouvez vous m'indiquer un site o? je pourrai trouver cela ? Jmol should not have trouble to run on OS/X; we have been using it inside Bioclipse for a long while, and most of the Bioclipse developers are running OS/X... What website in particular are you looking for? Where to download Jmol, or Java, or a website which uses Jmol? Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------ Message: 4 Date: Fri, 13 Feb 2009 16:03:34 +0100 From: "Angel Herraez" <[email protected]> Subject: Re: [Jmol-users] Bonds not showing in Jmol 11.6 To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=US-ASCII Hi Ewen That's pdb format, right? I've done a quick test and it's working for me in both 11.4.6 and 11.6.16 Check the column positions of the atom numbers, might be that. Not an explanation for your problem, but you could also dispose of CONECT records and use Jmol "connect" command -- it's cleaner and more flexible (partial bonds for example). And you can embed it in the pdb file if you don't want to run a separate script. http://wiki.jmol.org/index.php/File_formats#Script_inline_within_a_mol ecular_coordinates_file ------------------------------ Message: 5 Date: Fri, 13 Feb 2009 14:50:34 +0100 From: Amal CHLYEH <[email protected]> Subject: Re: [Jmol-users] Mac OS X To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed thank you very much Egon my problem is to download Jmol to visualize the molecules in 3D and which turns under Mac OS X. I did not find any site for that. Can you say to me where I can downloaded Jmol? thank you Amal Le 13 f?vr. 09 ? 15:30, Egon Willighagen a ?crit : > Hi Amal, > > 2009/2/13 Amal CHLYEH <[email protected]>: >> je voudrais utiliser un ligiciel de visualisation des mol?cules en 3D >> mais je ne trouve rien qui puisse aller avec Mac OS X. >> Pouvez vous m'indiquer un site o? je pourrai trouver cela ? > > Jmol should not have trouble to run on OS/X; we have been using it > inside Bioclipse for a long while, and most of the Bioclipse > developers are running OS/X... > > What website in particular are you looking for? Where to download > Jmol, or Java, or a website which uses Jmol? > > Egon > > -- > ---- > http://chem-bla-ics.blogspot.com/ > > ---------------------------------------------------------------------- > -------- > Open Source Business Conference (OSBC), March 24-25, 2009, San > Francisco, CA > -OSBC tackles the biggest issue in open source: Open Sourcing the > Enterprise > -Strategies to boost innovation and cut costs with open source > participation > -Receive a $600 discount off the registration fee with the source > code: SFAD > http://p.sf.net/sfu/XcvMzF8H > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Ce message a ?t? v?rifi? par MailScanner pour des virus ou des polluriels et rien de suspect n'a ?t? trouv?. MailScanner remercie transtec pour son soutien. ------------------------------ Message: 6 Date: Fri, 13 Feb 2009 16:10:41 +0100 From: "Angel Herraez" <[email protected]> Subject: Re: [Jmol-users] Mac OS X To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=US-ASCII > Can you say to me where I can downloaded Jmol? http://jmol.org and follow the links ------------------------------ Message: 7 Date: Fri, 13 Feb 2009 16:09:33 +0100 From: Rolf Huehne <[email protected]> Subject: Re: [Jmol-users] Mac OS X To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1 Amal CHLYEH wrote: > thank you very much Egon > my problem is to download Jmol to visualize the molecules in 3D and > which turns under Mac OS X. > I did not find any site for that. > Can you say to me where I can downloaded Jmol? > thank you You can download Jmol from the SourceForge download page at http://sourceforge.net/project/showfiles.php?group_id=23629 This page is also linked within the Homepage of Jmol at http://www.jmol.org/ Regards, Rolf ------------------------------ Message: 8 Date: Fri, 13 Feb 2009 16:19:54 +0100 From: Egon Willighagen <[email protected]> Subject: Re: [Jmol-users] Mac OS X To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1 On Fri, Feb 13, 2009 at 2:50 PM, Amal CHLYEH <[email protected]> wrote: > Can you say to me where I can downloaded Jmol? Go to: https://sourceforge.net/project/showfiles.php?group_id=23629&package_id= 16155&release_id=659510 and download the jmol-11.6.16-binary.zip and unzip it on your machine... It is not a OS/X specific executable, but a Java .jar file, which you can run with Java with: java -jar Jmol.jar Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------ Message: 9 Date: Fri, 13 Feb 2009 17:19:36 +0100 From: Paul Pillot <[email protected]> Subject: Re: [Jmol-users] Mac OS X To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Bonjour Amal, Jmol fonctionne bien avec MacOSX. Il existe 2 versions de Jmol : une application qui est accessible en double cliquant sur le fichier Jmol.jar de l'archive zip contenant le programme Jmol. L'autre version est une applet qui doit ?tre int?gr?e dans une page web pour fonctionner. Il existe des programmes en ligne qui incorporent Jmol et permettent de visualiser ainsi des mod?les 3D : protein explorer : http://chemapps.stolaf.edu/pe/protexpl/htm/index.htm qui est tr?s complet. Il existe autrement de tr?s nombreux autres logiciels offrant des possibilit?s de visualisation et de traitement tr?s avanc?es. Sous mac, j'utilise chimera http://www.cgl.ucsf.edu/chimera/ , il y a aussi VMD, Ballview, etc... Bon courage ! Paul Le 13 f?vr. 09 ? 14:03, Amal CHLYEH a ?crit : > Bonjour, > je voudrais utiliser un ligiciel de visualisation des mol?cules en 3D > mais je ne trouve rien qui puisse aller avec Mac OS X. > Pouvez vous m'indiquer un site o? je pourrai trouver cela ? > D'avance merci > > Pr. Amal CHLYEH > Universit? Cadi Ayyad > Facult? des Sciences > Marrakech MAROC > -- > Ce message a ?t? v?rifi? par MailScanner > pour des virus ou des polluriels et rien de > suspect n'a ?t? trouv?. > MailScanner remercie transtec pour son soutien. > > > ---------------------------------------------------------------------- > -------- > Open Source Business Conference (OSBC), March 24-25, 2009, San > Francisco, CA > -OSBC tackles the biggest issue in open source: Open Sourcing the > Enterprise > -Strategies to boost innovation and cut costs with open source > participation > -Receive a $600 discount off the registration fee with the source > code: SFAD > http://p.sf.net/sfu/XcvMzF8H > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------ ------------------------------------------------------------------------ ------ Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ------------------------------ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users End of Jmol-users Digest, Vol 33, Issue 19 ****************************************** ------------------------------------------------------------------------------ Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
