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Re: [ccp4bb] chiral volumes--2nd try |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: chiral volumes--2nd try From: Patrick Loll pat {- dot -} loll {- at -} DREXEL {- dot -} EDU Date: 2010-04-20 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.loll@drexelmed.edu CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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