Stereochemistry statistics
Hi All, I have a very naive question, but nobody I have asked has been able to give me a confident answer. When phenix calculates the stereochemistry statistics for a model, two of the statistics given are RMS(chirality) and RMS(planarity). What specific measurements are being calculated to produce these statistics, and what are the units for the numbers given? For example, is RMS(planarity) telling me the average distance out of plane for an atom that should be in plane? If this is the case I imagine the units are angstroms? Thanks for the explanation, Mike Thompson -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles [email protected]
Hi Mike,
When phenix calculates the stereochemistry statistics for a model, two of the statistics given are RMS(chirality) and RMS(planarity).
It is best to think of these as "RMSD" - root mean square differences. We have tables with "ideal" values that are compared with "model" values, e.g. angle_ideal and angled_model. The RMSD are sqrt( mean( (model_value-ideal_value)**2 ) ) Therefore the units of the RMSD values are the same as those of the individual values, as you suggest...
What specific measurements are being calculated to produce these statistics, and what are the units for the numbers given? For example, is RMS(planarity) telling me the average distance out of plane for an atom that should be in plane? If this is the case I imagine the units are angstroms?
Yes, that's right. (We compute a plane that minimizes the RMSD.) The chiral differences are computed as differences of volumes; the units are Angstrom**3. Four atoms are involved, labeled as "centre", "1", "2", "3". These are used to compute three vectors: a = 1 - centre b = 2 - centre c = 3 - centre The chiral volume is a.dot(b.cross(c)), using the vector dot product and cross product. Note that this is the same formula as used for computing unit cell volumes. See also: Hendrickson, W.A. (1985). Meth. Enzym. 115, 252-270. Ralf
Hi Mike, I hope you find answers here and in references inside: http://cci.lbl.gov/publications/download/iucrcompcomm_aug2004.pdf http://journals.iucr.org/d/issues/2004/12/01/ba5072/index.html http://journals.iucr.org/a/issues/1991/06/00/vs0099/vs0099.pdf http://journals.iucr.org/j/issues/1989/05/00/ms0269/ms0269.pdf Pavel. On 1/19/11 5:03 PM, [email protected] wrote:
Hi All,
I have a very naive question, but nobody I have asked has been able to give me a confident answer. When phenix calculates the stereochemistry statistics for a model, two of the statistics given are RMS(chirality) and RMS(planarity). What specific measurements are being calculated to produce these statistics, and what are the units for the numbers given? For example, is RMS(planarity) telling me the average distance out of plane for an atom that should be in plane? If this is the case I imagine the units are angstroms?
Thanks for the explanation,
Mike Thompson
participants (3)
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miket＠chem.ucla.edu -
Pavel Afonine -
Ralf W. Grosse-Kunstleve