Re: [Jmol-users] Jmol applet "blinking" during scripted animations with Safari
Just to follow up. You were correct, Bob - the blinking had nothing to do with Jmol. It was actually the CSS "tabs" on the top of the page (along with the slider control). A slight change in the CSS code that creates the tabs (removing the float property) appears to have fixed the problem. Dean On Wed, Apr 1, 2009 at 11:34 PM, Robert Hanson wrote: > Dean, it appears to me to be the slider control. Moving it triggers a > repaint of the applet, which not happening smoothly. It's possible that Jmol > is at fault. But I'm not sure. Try creating the applet with a different > background color. If you can avoid the white/black switch, perhaps it won't > be so noticeable. > > On Wed, Apr 1, 2009 at 9:44 PM, Dean Johnston wrote: > >> Jmol users, >> >> Has anybody else noticed the Jmol applet "blinking" (flashing black) when >> being scripted via Javascript in Safari? I've had some users complain with >> my website (http://symmetry.otterbein.edu/gallery), but I'm not sure if >> it's something specific I'm doing. It can be rather distracting since all >> my animations are run via Javascipt. >> >> I see the behavior in Safari 3 and Safari 4 (beta) on OS X. I don't see >> it with Firefox or with any Windows browser. I'm using OS X 10.5.6. The >> web site uses Jmol 11.6. I've tested with the latest Jmol release and see >> the same behavior. >> >> Thanks for any help or suggestions. >> >> Dean >> >> >> -- >> >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> 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 > > > -- > > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Internationalisation and localisation
Hi, We are currently using GNU gettext tools (.po files) for translating the applet and the application. All .po files are under SVN, http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/translation/ We also use Launchpad for the translations : https://translations.launchpad.net/jmol Nico On Thu, Apr 9, 2009 at 3:55 PM, Gerard Meijssen wrote: > Hoi, > At translatewiki.net we localise in over 300 languages. I am sure that you > have an extensive list of translations we may be able to extend this list. > FYI in our software we load from SVN for both Jmol and the StubManager so we > should use whatever is set up in SVN. > Thanks, >Gerard > > http://translatewiki.net/wiki/Translating:Group_statistics > > 2009/4/9 Robert Hanson > > Sure -- Jmol has quite an extensive set of translations. There is an >> efficient team that monitors this, and I think at this point we have all the >> core internationalization business in place for all phrases. Every once in a >> while we find a message that has yet to be translated. We use a modified GT >> system. >> >> On Thu, Apr 9, 2009 at 8:42 AM, Gerard Meijssen < >> gerard.meijs...@gmail.com> wrote: >> >>> Hoi, >>> I am involved in the internationalisation and localisation of MediaWiki >>> and its extensions. I can imagine that this might make a difference for Jmol >>> as well. >>> Thanks, >>> GerardM >>> >>> >>> -- >>> 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-users mailing list >>> Jmol-users@lists.sourceforge.net >>> 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 >> >> >> -- >> 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-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > 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-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Installing jmol
2009/4/9 Gerard Meijssen : > Hoi, > I am involved with creating test environments for MediaWiki and its > extensions. As I have blogged many times about Jmol. I want to have a script > that installs Jmol together with StubManager. I have this installed, now the > challenge is to demonstrate that it works. Currently 3 error messages show > up. I have done nothing yet about setting up the environment with variables > because in essence I am not a developer myself. > > http://fosdem.wikiation.nl/revisions/Brion/index.php/Special:Version Jmol is > installed here for now, this is a scratch install environment so it may not > be there in a few days time. > > At the moment I am involved in a project to bring protein data in a Semantic > MediaWiki environment. Much of the original data comes from Uniprot and the > UMLS. I would appreciate it if someone helps me with getting Jmol in a test > environment to work and, show me what data in Uniprot UMLS enables Jmol to > show its stuff. Hi Gerard, I don't know about UMLS, but UniProt is mapped to the PDB via a project called SIFTS http://www.ebi.ac.uk/msd/sifts/ http://www.ebi.ac.uk/msd/sifts/ftp.html Using SIFTS you should be able to discover the appropriate PDB file(s) for a given UniProt entry, and open Jmol on that file... The Jmol MW plugin can be pointed at a PDB file on an FTP server somewhere in response to a specific value on a page in the wiki. i.e. if your UniProt record sets a 'has structure=x' value in a template, then you should be able to fire up Jmol in response. However, I'm not sure how 'deep' the integration between the data in the UniProt record and the Jmol applet could run... potentially it could do a lot of nice things. One tool which integrates Jmol and sequence is called JalView (I work in the same lab as the current maintainer of Jalview). This java program allows you to click on the structure and have the residue highlighted in an alignment (i.e. an alignment provided by SIFTS). However, there is currently no JalView MW plugin (although there is a JalView applet). The most impressive Jmol MW integration site is Proteopedia, but I don't think they do anything with UniProt (yet). Out of interest, how hard was it to turn the Jmol applet into a MW plugin? Would it be easy to apply the same steps to the JalView applet? JalView already handles sequence feature / structure integration, so it could be easier to develop that plugin than to get Jmol working via sifts (but I'm not sure on that point). Good luck with your testing! Dan. > Thanks, > Gerard Meijssen (GerardM in the wiki world) > > -- > 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-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Internationalisation and localisation
Hoi, At translatewiki.net we localise in over 300 languages. I am sure that you have an extensive list of translations we may be able to extend this list. FYI in our software we load from SVN for both Jmol and the StubManager so we should use whatever is set up in SVN. Thanks, Gerard http://translatewiki.net/wiki/Translating:Group_statistics 2009/4/9 Robert Hanson > Sure -- Jmol has quite an extensive set of translations. There is an > efficient team that monitors this, and I think at this point we have all the > core internationalization business in place for all phrases. Every once in a > while we find a message that has yet to be translated. We use a modified GT > system. > > On Thu, Apr 9, 2009 at 8:42 AM, Gerard Meijssen > wrote: > >> Hoi, >> I am involved in the internationalisation and localisation of MediaWiki >> and its extensions. I can imagine that this might make a difference for Jmol >> as well. >> Thanks, >> GerardM >> >> >> -- >> 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-users mailing list >> Jmol-users@lists.sourceforge.net >> 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 > > > -- > 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-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Internationalisation and localisation
One more comment -- it's important that the Wiki use the default applet loading -- JmolApplet0.jar -- not JmolApplet.jar -- as that allows for a much faster load and a much more efficient localization. Bob On Thu, Apr 9, 2009 at 8:48 AM, Robert Hanson wrote: > Sure -- Jmol has quite an extensive set of translations. There is an > efficient team that monitors this, and I think at this point we have all the > core internationalization business in place for all phrases. Every once in a > while we find a message that has yet to be translated. We use a modified GT > system. > > On Thu, Apr 9, 2009 at 8:42 AM, Gerard Meijssen > wrote: > >> Hoi, >> I am involved in the internationalisation and localisation of MediaWiki >> and its extensions. I can imagine that this might make a difference for Jmol >> as well. >> Thanks, >> GerardM >> >> >> -- >> 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-users mailing list >> Jmol-users@lists.sourceforge.net >> 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 > -- 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 -- 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Internationalisation and localisation
Sure -- Jmol has quite an extensive set of translations. There is an efficient team that monitors this, and I think at this point we have all the core internationalization business in place for all phrases. Every once in a while we find a message that has yet to be translated. We use a modified GT system. On Thu, Apr 9, 2009 at 8:42 AM, Gerard Meijssen wrote: > Hoi, > I am involved in the internationalisation and localisation of MediaWiki and > its extensions. I can imagine that this might make a difference for Jmol as > well. > Thanks, > GerardM > > > -- > 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-users mailing list > Jmol-users@lists.sourceforge.net > 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 -- 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Internationalisation and localisation
Hoi, I am involved in the internationalisation and localisation of MediaWiki and its extensions. I can imagine that this might make a difference for Jmol as well. Thanks, GerardM -- 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Release of R.E.D. Server
Thanks, can you please add a comment specifically to Jmol users highlighting how Jmol can be used in relation to this server? Thanks. Bob -- 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 -- 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Installing jmol
Hoi, I am involved with creating test environments for MediaWiki and its extensions. As I have blogged many times about Jmol. I want to have a script that installs Jmol together with StubManager. I have this installed, now the challenge is to demonstrate that it works. Currently 3 error messages show up. I have done nothing yet about setting up the environment with variables because in essence I am not a developer myself. http://fosdem.wikiation.nl/revisions/Brion/index.php/Special:Version Jmol is installed here for now, this is a scratch install environment so it may not be there in a few days time. At the moment I am involved in a project to bring protein data in a Semantic MediaWiki environment. Much of the original data comes from Uniprot and the UMLS. I would appreciate it if someone helps me with getting Jmol in a test environment to work and, show me what data in Uniprot UMLS enables Jmol to show its stuff. Thanks, Gerard Meijssen (GerardM in the wiki world) -- 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] bug? Setting calculation of bonds on molecule load
Hi all, I would like to disable the automatic calculation of bonds on startup. This is needed for viewing large metal structures. There is an option in "edit"->"properties"->"Bonds" and then "Don't Compute Bonds". However: It doesn't seem to do anything. I tried setting autoBonds in ~HOME/.jmol/properties to false, true, 0, 1, off, on, that at least removes the "checked" sign in the properties menu, but calculation of bonds still occurs. I tried to look in the code a bit but couldn't find an easy solution. Using jmol 11.6.20. Any hints? -- Greetings, Pim http://www.molmod.com -- Greetings, Pim http://www.molmod.com -- 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Release of R.E.D. Server
Dear All, I am pleased to announce the release of R.E.D. Server available @ http://q4md-forcefieldtools.org/REDS/. R.E.D. Server provides the software and hardware (i. e. a cluster of computers) required for the derivation of highly effective and reproducible RESP and ESP atomic charge values embedded in force field libraries suitable for molecular dynamics simulations. R.E.D. Server interfaces the last stable version of the RESP ESP charge Derive program (R.E.D. IV April 2009 so far) developed by the q4md force field tools team, and provides the binaries for the last versions of the Gaussian, GAMESS-US, or the PC-GAMESS/Firefly program, and for the RESP program. More generally, the last developments in term of RESP and ESP charge derivation carried out by the q4md force field tools team will be provided through R.E.D. Server. The release of these new developments will be carried out from time to time, and the description of those last features released in R.E.D. Server is available at the "R.E.D. Server news" web page. By involving multiple molecules, multiple conformations and multiple orientations in charge derivation and by handling specific charge constraints during the fitting step, R.E.D. IV allows building complex force field topology database or FFTopDB corresponding to the simultaneous generation of numerous molecular fragments (N-terminal, C-terminal and central amino acid fragments, 5'- or Y'-terminal, 3'- or X'-terminal and central nucleotide fragments as well as monosaccharide and metal complex fragments) in a single execution. The all atom or united-carbon force field library model can be in-differentially generated. A procedure to study the impact of the various charge constraints required during the fitting step of a molecular fragment has been implemented allowing users to compare charge values, and thus to validate or reject charge sets. The use of R.E.D. Server and R.E.D. IV is described in Frequently Asked Questions http://q4md-forcefieldtools.org/REDS/faq.php as well as in a specific tutorial http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php. Academic users involved in non-profit research are authorized to use R.E.D. Server. The use of R.E.D. Server is provided at no cost after signing a license agreement. The PI (principal investigator or Director of a laboratory) and the PU (R.E.D. Server principal user) have to register and sign a license agreement to be authorized to use R.E.D. Server. A general public help is provided with the q4md-forcefieldtools mailing list. Any researcher can participate in this mailing list by answering and/or sending queries at q4md-...@q4md-forcefieldtools.org after registration at sy...@q4md-forcefieldtools.org. Archives of the q4md-fft mailing list are public. A private assistance is also available for registered users from the "Assistance" Service available at the R.E.D. Server Home page. We are registered in the AMBER and CCL mailing lists, and we will answer to the queries about the q4md force field tools in these mailing lists as well. The R.E.D. III.2 tools distributed in a standalone version at http://q4md-forcefieldtools.org/RED/, the RESP ESP charge DDataBase (or R.E.DD.B. http://q4md-forcefieldtools.org/REDDB/) which allows freely storing and distributing RESP and ESP charges embedded in force field libraries in the scientific community and R.E.D. Server constitute to the best of our knowledge unique tools. regards, F.-Y. Dupradeau --- http://q4md-forcefieldtools.org/FyD/ -- 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
