Bernhard and Ian, Since you ask, SHELXL defines a chiral volume as the volume of the 'unit-cell' that can be constructed using the three interatomic vectors from the atom in question. I think that I took this from PROLSQ, and that Bernhard's formula (which corresponds to the value of a determinant) should give the same answer. SHELXL restricts chiral volumes to cases where an atom makes exactly three bonds to other non-hydrogen atoms; hydrogen atoms are ignored. The sign is determined by evaluating the determinant with the rows representing the three vectors in the order of their ASCII codes, and so is independent of the order of the atoms in the input file. This means that the alpha carbon in the 19 standard chiral L-amino-acids will always have a chiral volume of about +2.5; it would have been confusing if I had used the Cahn-Ingold-Prelog R and S rules for the sign because of Cys. CB of Ile has a (SHELX) chiral volume of 2.495 but CB of Thr is -2.628. However the CHIV instruction in SHELXL also has other uses, e.g.
CHIV_VAL C CHIV_VAL 2.516 CA CHIV_VAL -2.622 CB This restrains the chiral volume of the carbonyl carbon to be zero (the default) with a default esd (0.1 A^3), i.e. restrains it to be planar. CB is not chiral for valine, but the above restraint makes sure that CG1 and CG2 are named conventionally (the RSCB now use this idea to check the naming of H-atoms in CH2 groups, which is one of the reasons why I always remove the hydrogens before depositing the structure (they are always recalculated anyway before use, e.g. by MolProbity). And if you wanted all the alpha-carbons for the alanines to have the same chiral volume but would like to refine its value, a SHELX 'free-variable' can be used (here #3): CHIV_ALA 31 CA (i.e. 1*fv(3)); if there is a D-Ala in the structure as well: CHIV_DAL 29 CA (i.e. -1*fv(3)). I think that I will have to add all this to Kay's Wiki. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Sat, 4 Apr 2009, Ian Tickle wrote: > Bernhard > > Refmac doesn't specify a target value for the chiral volume, it just > specifies 'positive' or 'negative'. It presumably uses the chiral > volume computed from the input co-ords as the target, so this is updated > as the refinement proceeds. I guess the goal isn't to restrain the > geometry to a particular value of the chiral volume, since that's > already determined by the bond lengths & angles (apart from the sign > ambiguity obviously), but rather just to prevent it from inverting to > the other hand. Note that it doesn't have to be a chiral centre to use > a chiral volume restraint, for a non-chiral centre where inversion is > equivalent to rotation (if you ignore the atom labels), it can still be > used to prevent inversion, since that would result in atom labels being > swapped (all non-planar atom centres are chiral if you include the atom > labels!). > > Don't know how Shel-X handles it, I guess George will answer that. > > Cheers > > -- Ian > > > -----Original Message----- > > From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] > On > > Behalf Of Bernhard Rupp > > Sent: 04 April 2009 05:21 > > To: CCP4BB@jiscmail.ac.uk > > Subject: chiral volume target value > > > > Dear All, > > > > assuming the chiral volume definition with r() a Cartesian position > vector > > > > Vc = [r(N)-r(Ca)]*([r(C)-r(Ca)]x[r(Cb)-r(Ca)]) > > > > I always get about -0.65 A**3 > > > > Is this correct? Are there any target values? > > > > In a SHELX manual I read + 2.5 for the chiral volume - seems to > > be different. > > > > (not to be confused with the pseudo-torsion target of +34 deg) > > > > Thx, BR > > ----------------------------------------------------------------- > > Bernhard Rupp > > b...@ruppweb.org > > http://www.ruppweb.org/ > > ----------------------------------------------------------------- > > The hard part about playing chicken > > is to know when to flinch > > ----------------------------------------------------------------- > > > > Disclaimer > This communication is confidential and may contain privileged information > intended solely for the named addressee(s). It may not be used or disclosed > except for the purpose for which it has been sent. If you are not the > intended recipient you must not review, use, disclose, copy, distribute or > take any action in reliance upon it. If you have received this communication > in error, please notify Astex Therapeutics Ltd by emailing > i.tic...@astex-therapeutics.com and destroy all copies of the message and any > attached documents. > Astex Therapeutics Ltd monitors, controls and protects all its messaging > traffic in compliance with its corporate email policy. The Company accepts no > liability or responsibility for any onward transmission or use of emails and > attachments having left the Astex Therapeutics domain. Unless expressly > stated, opinions in this message are those of the individual sender and not > of Astex Therapeutics Ltd. The recipient should check this email and any > attachments for the presence of computer viruses. Astex Therapeutics Ltd > accepts no liability for damage caused by any virus transmitted by this > email. E-mail is susceptible to data corruption, interception, unauthorized > amendment, and tampering, Astex Therapeutics Ltd only send and receive > e-mails on the basis that the Company is not liable for any such alteration > or any consequences thereof. > Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, > Cambridge CB4 0QA under number 3751674 >
