There's no user support specifically for Aalto Wiki. Aalto Service Desk servicedesk(a) aalto.fi is where to contact.Īalto Service Desk has forwarded the question to the service providers of Aalto Wiki to check whether the platform handles tools for viewing 3D structures. Tried with the secured Jmol link, e.g., but there's no Confluence macro that displays the 3D model.
Other option is to install JSmol on the site but I don't think that is possible unless there is an official Confluence plugin. Since Jalview 2.3, Jmol has been integrated into Jalview for interactively viewing structures opened by selecting the 'StructureView PDB entry:' option in the sequence id pop-up menu (if you cant see this, then you need to associate a PDB structure with the sequence). Setting the wiki to public may work.įor real crystal structures with pdb id (pdb id in place of xxxx): If this is used the models need to be hosted on a public location so the Jmol plugin can find them. The probe radius can be defined using the set radius command. Jmol, as Rasmol, uses a sphere with 1.2 radius for water Chime uses 1.2 for dots and 1.4 for surfaces. This method defines the interface between CDK and Jmol as a plain text file format, e.g. Definition: probe (solvent probe) is a sphere that approximates the effective size of the solvent molecule.
Jmol viewer mac os#
It works on multiple platforms, including Windows, Mac OS X, and Linux/Unix systems. This page will introduce ways in which Jmol can be integrated into CDK programs, so that the first can be used as a 3D viewer for the CDK data structures. However, I could not get the JavaScript commands to work with the wiki platform. Jmol is a free, open-source molecule viewer for chemistry and biochemistry.
The easiest way to add a Jmol viewer would be these instructions because they don't need installations on the wiki.
Confluence makes it really hard or impossible to add custom features, such as Jmol viewers.
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