[Chimera-users] New Residue-interaction network MD movie plugin

rswett at chem.wayne.edu rswett at chem.wayne.edu
Fri Sep 19 07:22:32 PDT 2014

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.


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

> On Sep 18, 2014, at 11:32 AM, rswett at 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.

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