[cmview-devel] CMView application note and testing

lappe lappe at molgen.mpg.de
Fri Dec 10 17:24:05 EST 2010

Hey guys - just completed the installation on Mac (OSX 10.5.8) - startup,
loading & basics with pymol & dssp are working fine - notes & details see
below - except Dali (still downloading GTG) - do we need all of that or is
DaliLite.tar.gz sufficient ? I mean 5.7 (GTG) + 1.2 GB (SQL dump) is pretty
hefty, even compared to our background data ;) 
cheers .\\ichael 


CMView2 MAC OSX Installation notes : 

System requirements: 
Since CMView2 needs Java 1.6 this means it will run on Mac OS X v 10.5.2
or later. 

To make sure Java1.6 is there and active run the Java Preference Pane  
/Applications/Utilities/Java Preferences 
under "General" verify that the Java Applications version is Java SE 6. 
by making sure the checkbox is ON and then drag this entry 
to the top of the list if it is not up there already.
If 1.6 is not there just running a Software Update should fix it. 
Now double-cklicking the CMView2.jar in finder should launch just fine -  
of course given the cmview.cfg has been set-up according to your system. 
All messages and errors can be seen in the console (which is also found in


The Mac-specific settings in the configuration.file involve telling CMView

where to find other executables like dssp for secondary structure
or pymol for the 3D display. For automatic launching of pymol on startup
shutdown alongside CMView the corresponding line in cmview.cfg has to 
point *INTO* the application-folder of pymol to the actual executable
(reminder: Applications in OSX might look like a single file although they

actually might be a folder containing additional resources of the program,

which is defintely true for PyMol). 
For example, if you have your MacPYMOL is installed in the default
location in 
/Applications, the configuration should read


Some additional nice, but non-critical touches  

* Equipping cmview with a cool icon 
right-click on cmview2.jar -> click "Get Info 
On top left next to the name you can see the icon (the java coffee cup by
which gets a blueish frame if you click it - leave it "activated" like
Now you can drag a .png file onto it which will become the new icon and
appear under "preview" below - now you can close the window and the icon
have changed accordingly in the finder - an cmviewicon.png can be found
_here_ . 

* like any other application, you can drag the jar into the dock
(in the section where "Documents" or "Downloads" are after the dashed
to have it ready for immediate launch
Installing DSSP 
The Mac-executable from http://swift.cmbi.ru.nl/gv/dssp/
gives you a file named DSSP_MAC.EXE which doesn't really work (at least
for me)
so downloading the source from the above location and compiling it with
was the only way. Afterwards, just point CMView to the DSSP executable in
the config.file 
(???check this) alternatively, turn it off by  

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