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
