Re: [Jmol-users] Add hydrogens to PDBs after they are loaded

2015-04-20 Thread Brenton Horne
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 , and , with being the only one that fetches the PDB the like I'd like it to.

Re: [Jmol-users] Add hydrogens to PDBs after they are loaded

2015-04-20 Thread Jaime Prilusky
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 wrote: > > Hi, > > I have been using the JSmol extension for MediaWiki and I'd like

[Jmol-users] Add hydrogens to PDBs after they are loaded

2015-04-20 Thread Brenton Horne
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 com

Re: [Jmol-users] mmCIF - higher numbers refused as chain ids

2015-04-20 Thread Rolf Huehne
Am 20.04.15 um 20:25 schrieb Robert Hanson: > Written before the I am not seeing this problem. I tried 14.2 and 14.3 > with a file that for which I changed > > _atom_site.auth_asym_id (standard chain designation) > > or > > _atom_site.label_asym_id (used with FILTER "noAuthorChains") > > with num

Re: [Jmol-users] mmCIF - higher numbers refused as chain ids

2015-04-20 Thread Robert Hanson
Written before the I am not seeing this problem. I tried 14.2 and 14.3 with a file that for which I changed _atom_site.auth_asym_id (standard chain designation) or _atom_site.label_asym_id (used with FILTER "noAuthorChains") with numbers like "3480" and "3489" and found no problems. load t.c

Re: [Jmol-users] mmCIF - higher numbers refused as chain ids

2015-04-20 Thread Rolf Huehne
On 04/20/2015 03:44 PM, Robert Hanson wrote: > how unusual! I will look into it. Definitely a bug. I can't imagine why it > is doing that > It looks like I should have been more precise in my description. The mmCIF data were actually loaded from a variable and not from a file. This is the cas

Re: [Jmol-users] mmCIF - higher numbers refused as chain ids

2015-04-20 Thread Robert Hanson
how unusual! I will look into it. Definitely a bug. I can't imagine why it is doing that On Mon, Apr 20, 2015 at 8:42 AM, Rolf Huehne wrote: > Hi all, > > the mmCIF format generally allows multicharacter chain ids. This should > also include numeric characters. > But Jmol 14.3.13_2015.04.17

[Jmol-users] mmCIF - higher numbers refused as chain ids

2015-04-20 Thread Rolf Huehne
Hi all, the mmCIF format generally allows multicharacter chain ids. This should also include numeric characters. But Jmol 14.3.13_2015.04.17 seems to refuse to load multicharacter chain ids if they consist only of numerical characters. I tried to load an mmCIF file with several thousand chains