Miguel,
Thanks for your informative reply. The questions you raise go to the heart of the matter, and I hope will provoke useful suggestions.
I do not believe that Pauling used radii different from the accepted vdw values of the time. I have looked in a number of more recent listings and find the following values, some of which are significantly different from those you have noted.
Hydrogen 1,20 angstroms Carbon 1.70 Nitrogen 1.55 Oxygen 1.52
Clearly, the heavier atom radii used by Jmol are proportionally larger, relative to hydrogen, than the radii I have cited or those used by RasMol. This may account for the difference in appearance of spacefilled models.
Bill
Miguel wrote:
I looked at the values for vdw radii used by Jmol. The table below compares a few elements:
Element RasMol vdw RasMol united Jmol/OpenBabel vdw ------- ---------- ------------- ------------------ H 1.100 N/A 1.200 C 1.548 1.872 1.950 N 1.400 1.507 1.850 O 1.348 1.400 1.700 P 1.880 N/A 2.080 S 1.808 1.848 2.000
We can see that the Jmol vdw values are larger than the RasMol vdw and the RasMol united radii for all of these elements.
I took the Jmol values from OpenBabel (as documented and referenced in the Jmol source code). I do not know where they came from.
However, now that I think about it, it is not clear to me whether or not these values in OpenBabel are even used ... Certainly the covalent radii are used, but the vdw radii may not even be used.
It now seems to me that Jmol should take these vdw radii from a standard reference of vdw radii ... like the CRC, perhaps?
Q: Is there a 'standard reference' for VDW radii? Perhaps the CRC?
Q: Do people agree that we should use these values as the defaults
Assuming that we get the issue above resolved, and that Jmol starts using some 'published/standard' vdw radius table ...
Q: Bill, do you believe that there is a 'Pauling' radius which is substantially different from the VDW radius?
Miguel
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