Nvm, it worked perfectly, thanks. On 21/04/2015 4:41 PM, Brenton Horne wrote: > OK, but keeping in mind I'd like text (e.g., 2ACE for your example) > hyperlinked with a JavaScript popup containing the JSmol applet not a > JSmol applet embedded in the Wiki page. The only way I know to do this > is via <jmolFile>, <jmolPdb> and <jmolSmiles>, with <jmolPdb> being the > only one that fetches the PDB the like I'd like it to. As I understand > it <jmolPdb> fetches the PDB file before executing any script inputs. As > you saying that, for example: > > <jmolPdb script = "set pdbAddHydrogens true; load = 3U5K">3U5K</jmolPdb> > > will load 3U5K with hydrogens added? > > Thanks for your time, > Brenton > > On 21/04/2015 4:26 PM, Jaime Prilusky wrote: >> Brenton, >> >> On the script you currently use, you should be able to add pdbAddHydrogens >> before loading, as here: >> >> set pdbAddHydrogens true; load= 2ace; >> >> Regards, >> Jaim >> >>> On Apr 21, 2015, at 8:56 AM, Brenton Horne <brentonho...@ymail.com> wrote: >>> >>> Hi, >>> >>> I have been using the JSmol extension for MediaWiki and I'd like to know >>> what script argument I need in order for hydrogens to be added to a >>> fetched PDB file. But as I can't run commands for this extension before >>> the PDB is fetched (e.g., I'd use set pdbAddHydrogens TRUE if I could >>> run commands before the PDB was loaded) because I'm using <jmolPdb> tags >>> I'm left asking which commands I can run after fetching the PDB file >>> that will add hydrogens to the ligands and solvent. >>> >>> Thanks for your time, >>> Brenton >>> >>> ------------------------------------------------------------------------------ >>> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT >>> Develop your own process in accordance with the BPMN 2 standard >>> Learn Process modeling best practices with Bonita BPM through live exercises >>> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ >>> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF >>> _______________________________________________ >>> Jmol-users mailing list >>> Jmol-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >> ------------------------------------------------------------------------------ >> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT >> Develop your own process in accordance with the BPMN 2 standard >> Learn Process modeling best practices with Bonita BPM through live exercises >> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ >> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > ------------------------------------------------------------------------------ > BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT > Develop your own process in accordance with the BPMN 2 standard > Learn Process modeling best practices with Bonita BPM through live exercises > http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ > source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users >
------------------------------------------------------------------------------ BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
