Dear Michael, 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 sequence:
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, the
first line should be the '962', and save it with the .mol extension).
962
molecule 2D
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
M END
2) I opened this molecule in PyMOL, and displayed it with line
representation.
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 EXACTLY
to the sphere of the oxygen.
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. So I
don't understand how you came to the conclusion that there is a mismatch
between PyMOL values and experimental values.
Best regards,
Greg
-----Original Message-----
From: Michael Weber [mailto:web...@staff.uni-marburg.de]
Sent: vendredi, 30. juin 2006 08:23
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] spheres representation and atomic / ionic radii
Hi,
I have a question concerning the "spheres" representation. According to my
rough estimation the spheres drawn for individual atoms/ions don't seem not
match experimental atomic/ionic radii if I compare different elements. Is
that correct (I quickly checked for oxygen, phosphorus and magnesium2+)?
Furthermore, is it possible to manually assign radii to selected atoms?
Best regards,
Michael.
<<attachment: mol.png>>
