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 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 <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
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 ------------------------------------------------------------------------
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Michael Zimmermann -
Tom Goddard