I do not agree with you; I never observed any variation between sphere
representation and experimental data.
But to test the accuracy of the sphere size, I did the following =
1) I created a molecule composed of one hydrogen and one oxygen, with a
"fake" distance of 1.52 A between the two atoms. Here is the MOL file
corresponding to this molecule (you might save it using any text editor, =
first line should be the '962', and save it with the .mol extension).
2 1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.5200 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2) I opened this molecule in PyMOL, and displayed it with line
3) I created a new object from the O only, displayed as sphere (with a
transparency of 0.5).
4) Ray-tracing... gives the image attached to this e-mail.
One can see that the O-H line, having a length of 1.52A, corresponds =
to the sphere of the oxygen.=20
I checked using the same procedure the sphere size of Mg and here I also
obtained a perfect match between a bond length of 1.73A and the sphere. =
don't understand how you came to the conclusion that there is a mismatch
between PyMOL values and experimental values.
From: Michael Weber [mailto:weberm@...
Sent: vendredi, 30. juin 2006 08:23
Subject: [PyMOL] spheres representation and atomic / ionic radii
I have a question concerning the "spheres" representation. According to =
rough estimation the spheres drawn for individual atoms/ions don't seem =
match experimental atomic/ionic radii if I compare different elements. =
that correct (I quickly checked for oxygen, phosphorus and magnesium2+)? =
Furthermore, is it possible to manually assign radii to selected atoms?