Dear Chimera Staff,<br><br>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 <a href="http://emdatabank.org">emdatabank.org</a> 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.<br>
<br>>>> import chimera<br>>>> opened = chimera.openModels.open('C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\\ribosome\\70s.pdb')<br>>>> mol = opened[0]<br>>>> from chimera.colorTable import getColorByName<br>
>>> red = getColorByName('red')<br>>>> mol.color = red<br>Traceback (most recent call last):<br> File "<pyshell#42>", line 1, in <module><br> mol.color = red<br>ValueError: underlying C++ Molecule object is missing<br>
<br>Why is there a module missing? How do I find out what module is missing and add it?<br><br>>>> <a href="http://red.name">red.name</a><br><built-in method name of _chimera.MaterialColor object at 0x0F1AAF38><br>
>>> red.rgba<br><built-in method rgba of _chimera.MaterialColor object at 0x0F1AAF38><br><br>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?<br>
<br>>>> ATOMS = mol.atoms<br>Traceback (most recent call last):<br> File "<pyshell#54>", line 1, in <module><br> ATOMS = mol.atoms<br>ValueError: underlying C++ Molecule object is missing<br>
<br>Again, why is a module missing, how do I find out what module is missing, and how do I add it?<br><br>Thank you,<br><br>Michael Z<br>