Hi Michael, The error message is that the "Molecule" is missing. That suggests that you closed the molecule (e.g using File / Close Session or the Model Panel dialog). You can't close the molecule and still access it from Python. To show the color name use: >>> red.name() 'red' If you type just red.name as you did it says that is a "built-in method", in other words a function, so you have to call the function by adding the parentheses (). Tom Michael Zimmermann wrote:
Dear Chimera Staff,
I have been trying to learn to use your object model. My goal is to read in an electron density map in CCP4 format downloaded from emdatabank.org <http://emdatabank.org> and parse out the 3D matrix of electron density values. However, to get started I was trying to just access atomic information in a sample PDB format file (like atomic coordinates). Running through a few of your examples though has proven confusing to me. The following are commands that I have entered into the IDLE. I am using alpha version 1.3 build 2577.
import chimera opened = chimera.openModels.open('C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\\ribosome\\70s.pdb') mol = opened[0] from chimera.colorTable import getColorByName red = getColorByName('red') mol.color = red Traceback (most recent call last): File "<pyshell#42>", line 1, in <module> mol.color = red ValueError: underlying C++ Molecule object is missing
Why is there a module missing? How do I find out what module is missing and add it?
red.name <http://red.name> <built-in method name of _chimera.MaterialColor object at 0x0F1AAF38> red.rgba <built-in method rgba of _chimera.MaterialColor object at 0x0F1AAF38>
What if I want the value displayed rather than the object's ID? Is there a get method that has to be invoked? What would the syntax be?
ATOMS = mol.atoms Traceback (most recent call last): File "<pyshell#54>", line 1, in <module> ATOMS = mol.atoms ValueError: underlying C++ Molecule object is missing
Again, why is a module missing, how do I find out what module is missing, and how do I add it?
Thank you,
Michael Z ------------------------------------------------------------------------
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