Joel,
Arrrrgh. I can honestly say that this explanation never occurred to
me, even though it is consistent with the data (But come on, any
introductory organic chem text explains the R/S rules by moving from
atom 2 to 3 to 4, and not by jumping from 2 to 4...surely you would
follow the same convention in the refmac documentation, right?)
What amazes me is my inability to find ANY documentation that actually
explains the meaning of terms in the CIF used to define chiral
volumes. OK, some of the terms ARE found in the mmCIF dictionary, but
others seem made-up, like "_chem_comp_chir.atom_id_1." Given that both
refmac and phenix rely upon upon these libraries for determining
geometries, you'd think that somewhere the terms would be defined
explicitly.
As several posters have pointed out, the triple scalar product is of
course the correct way to define the chiral volume; but my point is
that if you don't know which atoms the program is assigning to which
vector, you're still in a pickle...
Pat
On 20 Apr 2010, at 3:51 PM, Bard, Joel wrote:
Hi Patrick-
I feel your pain having gone through exactly the same problem. It all
has to do with the definition of "When the eye goes from atom 2 to
atom
4". I think we both assumed that this meant from 2 to 4 via 3 but I
guess it doesn't. The ful text of my 2004 post:
I think that two of the numbers are reversed in Figure 3 of the chiral
center documentation for refmac5:
http://www.ccp4.ac.uk/dist/html/refmac5/theory/chiral.html
If one follows the "Procedure to find the sign of a chiral centre"
with
reference to the figure the eye would move from atom 2 through atom
3 to
atom 4 as it traveled clockwise. This would generate a left handed
coordinate system if atom 1 was behind the plane of the web browser so
the sign of the chiral volume would be negative rather than positive
as
the text says. Switching the labels of atoms 2 and 3 (or 2 and 4 or 3
and 4 but 2 and 3 make it easier to visualize the right-hand-rule)
would
make it work.
It seems like a very little thing but I'm feeble-minded enough to have
spent more time than I'd like to admit trying to figure out why a
little
program I'd written was coming up with the wrong sign for the chiral
volume when it had been correct the whole time. Of course I should
have
realized that it would be absurd for the statement: "When the eye goes
from atom2 to atom4 it should travel clockwise," to mean "When the eye
goes from atom2 to atom4 by passing through atom3 it should travel
clockwise". It might be worth fixing, though, since I know for a fact
that there are other people out there who are almost as easily
confused
as I am.
Cheers,
Joel
---------------------------------------------------------------------------------------
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA
(215) 762-7706
pat.l...@drexelmed.edu
