Hi Armida, I just tried the script in Chimera 1.3 and in a recent daily build (1.4) and it worked in both. I'm guessing that when you tried it, Chimera did not know the file type of the script because it was not named ending with ".py". If you look at the link below, even though the mail program names the file "attachment.ksh", the original name is "inertiapdb.py". You could name it that or actually anything that ends in .py and then it should work. For example, I saved the script file to my Desktop and named it inertiapdb.py. Then I started Chimera, then opened a PDB file, then used "File... Open" in the menu to open inertiapdb.py -- an ellipsoid is shown in the Chimera window and numerical information is shown in the Reply Log. I hope this helps, ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On May 14, 2009, at 6:42 AM, A. Di Fenza wrote:
Hi Tom, I saw your message on the web and I tried to use your script on Chimera 1.3. Unfortunately it does not work, it give me the following message:
0 models opened
Do you think it is because of the Chimera version? Do you have suggestion?
Thank you very much, Armida
Oops. That script I posted for calculating the inertia of a molecule had some problems. The printed matrix of axes was transposed though the correct axes were used for the displayed ellipsoid. Also I was using inertia matrix I_ij = sum_over_k(m_k*r_ki*r_kj) omitting the diagonal term. Should have been I_ij = sum_over_k(m_k*(|r_k| - r_ki*r_kj)). And finally I incorrectly computed the ellipsoid size along each axis. Everything was a little bit wrong. Here's the fixed version. Tested in Chimera version 1.2500 but should work with earlier versions.
Tom