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 Quoting Eric Pettersen <pett@cgl.ucsf.edu>:

On Sep 18, 2014, at 11:32 AM, rswett@chem.wayne.edu wrote:

...

Hey all, I'm trying to visualize an RIN from a dynamics run using the new addition to the Trajectory tools. Cytoscape isn't playing nice with launching chimera, so I was wondering how difficult it would be to save the calculated network to load independently in cytoscape? Currently the calculation runs just fine, but I can't save the output. Is there a command line way to do it? Any other suggestions?

Hi Rebecca, If you start Chimera from a shell, the residue-interaction tool will print out the path names of the files (and some other info) to the shell when you click Apply. On Linux it should be obvious how to start Chimera from the shell. Info for how to do it on Windows and Mac is at the end of this message. The files are:

1) <some temp name>_network.txt: network file, which you can use File->Import->Network->File in Cytoscape to open.

2) <some temp name>_nattr.txt: node attribute file: which you could open with File->Import->Table->File in Cytoscape, but is probably superfluous if Cytoscape isn't running in conjunction with Chimera.

3) <some temp name>_netviz.xml: network visualization style file, which you can import with File->Import->Vizmap File and which will define a "MD residue interactions" VizMapper style, which you could apply if you wanted.

However, the fact of the matter is that the whole shebang is considerably more useful if Chimera and Cytoscape are running together. First off, if connected to Chimera the nodes will be laid out spatially the same way they are depicted in Chimera (all with a Z of 0 of course) so it's immediately easier to tell where various interactions occur in the structure. Without Chimera, the nodes will be laid out in a square array, which you could change with various layout algorithms, but none of which will place them as they appear in the Chimera window. Second, without Chimera selecting nodes in Cytoscape won't select them in Chimera (obviously) and vice versa. Still it's better than nothing I suppose. It would be better if you could get StructureViz to launch Chimera. In not-extremely-old versions of StructureViz there is a "Path to chimera executable" setting where you can tell it where Chimera is. Were you already doing that and it wasn't working?

--Eric

Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

Shell on Mac: open the Terminal app (in Applications/Utilities). Drag and drop the Chimera icon onto Terminal. This should cause the path to Chimera.app to show up in Terminal. Append the text "/Contents/Resources/bin/chimera" to it (no quotes and no spaces between). Hit Return.

Shell on Windows: if you have Cygwin installed, use that and you should already know what to do. Otherwise, right click on the Chimera icon and select Properties. In the Shortcut field add " --debug" after the final quote [no quotes, but with a space before the first dash]. This will cause a text window to come up as your start Chimera. The text window will have the file name output when the time comes.