So to get thermal ellipsoids to display from a .cif file (as opposed to a .pdb) it looks like I need version 1.50 or greater of Chimera, but it looks like versions of Chimera above 1.4x don't seem to run on my Mac (I have system 10.4.11). What OSX system version do I need so that I can run a version of chimera that I can get thermal ellipsoids to display from a .cif file? Or, conversely is there a way I can get one of the more recent daily builds to run on OSX system 10.4.11? --Nat (Nathaniel Sherden) California Institute of Technology
On Mar 31, 2010, at 4:34 PM, sherden@caltech.edu wrote:
So to get thermal ellipsoids to display from a .cif file (as opposed to a .pdb) it looks like I need version 1.50 or greater of Chimera, but it looks like versions of Chimera above 1.4x don't seem to run on my Mac (I have system 10.4.11). What OSX system version do I need so that I can run a version of chimera that I can get thermal ellipsoids to display from a .cif file? Or, conversely is there a way I can get one of the more recent daily builds to run on OSX system 10.4.11?
Hi Nat, As you just encountered, the Chimera 1.4 series of releases are the last to support OS X 10.4. So you can't run Chimera 1.5+ without upgrading your OS X. Nonetheless, the changes made to support thermal ellipsoids in CIF files were all in the Python layer, so you should be able to drop a Python file with the changes into your 1.4 distribution and I think it should just work. I've attached the relevant file (__init__.py). You need to put it inside your 1.4 version of Chimera. Do this by right-clicking on the Chimera app in your Finder and choosing "Show Package Contents" from the popup menu. This will bring up a new Finder window. Navigate to Contents/Resources/share/ mmCIF. Replace the __init__.py file in there with the attached __init__.py. Restart Chimera and cross your fingers. Despite this possibly working I recommend upgrading to the 1.5 release whenever feasible since there are some nice improvements in the Thermal Ellipsoids tool that you will otherwise be missing. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Wonderful, that worked very well. Thanks a bunch. --Nat
On Mar 31, 2010, at 4:34 PM, sherden@caltech.edu wrote:
So to get thermal ellipsoids to display from a .cif file (as opposed to a .pdb) it looks like I need version 1.50 or greater of Chimera, but it looks like versions of Chimera above 1.4x don't seem to run on my Mac (I have system 10.4.11). What OSX system version do I need so that I can run a version of chimera that I can get thermal ellipsoids to display from a .cif file? Or, conversely is there a way I can get one of the more recent daily builds to run on OSX system 10.4.11?
Hi Nat, As you just encountered, the Chimera 1.4 series of releases are the last to support OS X 10.4. So you can't run Chimera 1.5+ without upgrading your OS X. Nonetheless, the changes made to support thermal ellipsoids in CIF files were all in the Python layer, so you should be able to drop a Python file with the changes into your 1.4 distribution and I think it should just work. I've attached the relevant file (__init__.py). You need to put it inside your 1.4 version of Chimera. Do this by right-clicking on the Chimera app in your Finder and choosing "Show Package Contents" from the popup menu. This will bring up a new Finder window. Navigate to Contents/Resources/share/ mmCIF. Replace the __init__.py file in there with the attached __init__.py. Restart Chimera and cross your fingers. Despite this possibly working I recommend upgrading to the 1.5 release whenever feasible since there are some nice improvements in the Thermal Ellipsoids tool that you will otherwise be missing.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
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Eric Pettersen -
sherden＠caltech.edu