[Chimera-users] Principal axis of inertia
A. Di Fenza
armida.difenza at sns.it
Fri May 15 02:38:54 PDT 2009
your guess was perfectly right! Thank you very much for the detailed
instructions it is the first time I use Chimera and that was what I
needed, now it works.
I have a question about the algorithm. As far as I have understood, the
script looks at the element name, say CA or N or C, to assign the atom
mass. So that if I have a pdb made of CA atoms only, the atom masses
used in the inertia matrix calculation are all the same. Is this right?
I need to be sure because I calculated with your script the inertia
matrix for the same protein first with all-atom and then with only the
CA, and I got that they are very similar although using the same mass
for all the atoms is a quite big approximation.
Thank you very much for your help!
Elaine Meng wrote:
> 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 at cgl.ucsf.edu
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 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
>> Thank you very much,
>> Oops. That script I posted for calculating the inertia of a molecule
>> had some problems. The printed matrix of axes was transposed though
>> 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)).
>> 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.
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>> Name: inertiapdb.py
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