Hi Rebecca, Sorry about the Cytoscape-Chimera connection difficulties. Our Cytoscape expert (and structureViz developer) Scooter Morris would normally be the one to address this, but he’s away for a few weeks. I’ll try to make sure he sees your message when he’s back on email. Best, Elaine On Sep 19, 2014, at 7:22 AM, rswett@chem.wayne.edu wrote:
Awesome, thanks for the suggestions. I'll try that. And yes, I agree I would love to be able to launch Chimera from inside Cytoscape, but it wasn't working. Believe me I tried. On both linux and windows. Entering the path doesn't work, either to the directory OR the executable, adding structureViz.chimeraPath in the properties doesn't work (found that one on an old tutorial). Running it with elevated permissions doesn't work. Accessing apps via the network is a no-go (that's likely my industry firewall), so I had to find a workaround to even download the apps from the website as the "install" button tries to communicate with Cytoscape and ends up going nowhere. But yes, for now I"ll try running things command line with linux. And as far as versions go, these were shiny-new ones downloaded yesterday.
Thanks! Rebecca