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Re: [ccp4bb] RMSD |
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CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 14 March 2007Subject: Re: RMSD From: Dirk Kostrewa dirk {- dot -} kostrewa {- at -} PSI {- dot -} CH Date: 2007-03-14 I vaguely remember differences between X-PLOR/CNS, TNT, REFMAC and WHAT_CHECK, especially for the carbonyl carbon-oxygen bond lenghths, but also some other values. I can't tell you anymore what the actual differences were. REFMAC and TNT use libraries that define directly the bond lenghths (etc.) and their SDs, whereas X-PLOR/CNS uses an energy-parametrization of bond lengths (etc.). Differences come either from a wrong assignment of atom types (like aromatic C, sp3-hybridized C, ...) to the atom names of amino acids, or wrong parametrizaiton, or from using more up-to-date values for specific bond lenghts. Especially, the carbonyl bond mentioned above seems to be non-optimal in the original Engh & Huber library, compared to values derived from atomic resolution crystal structures of proteins. Given the numbers of atomic resolution protein structures in the data bank, I think, it would be a good idea to derive a new Engh & Huber type set of stereochemical parameters directly from protein structures. Best regards, Dirk. Tim Gruene wrote: > Hello, > > I would love to learn how "differently" one can implement the difference > between two numbers? Or are you referring to 'versions'? > > Cheers, Tim > > -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > > On Wed, 14 Mar 2007, Dirk Kostrewa wrote: > >> Dear John, >> >> I don't know how different the RMSD values are, and whether the >> calculated estimates are with or without hydrogen atoms (this can make >> a difference). In principle, both programs use the Engh & Huber >> stereochemistry library, but I've observed in the past that different >> programs used slightly different "implementations" of this library, >> resulting in different RMSD values, although they should all be the >> same ... >> >> Good luck, >> >> Dirk. >> >> john kryst wrote: >>> Hi ccp4bb !!! >>> >>> Does the rmsd estimation (for eg. rmsd_bonds ) depends on the program >>> we use >>> ?? >>> >>> Example : shifting from Refmac to CNS. There appears to be an >>> increase in >>> rmsd of bonds even without refining the structure in CNS. Is the >>> estimation >>> methods are different or am i doing something wrong !! >>> >>> Thanks for your valuable inputs. >>> >>> regards >>> john >>> >> >> >> -- >> >> **************************************** >> Dirk Kostrewa >> Paul Scherrer Institut >> Biomolecular Research, OFLC/110 >> CH-5232 Villigen PSI, Switzerland >> Phone: +41-56-310-4722 >> Fax: +41-56-310-5288 >> E-mail: dirk.kostrewa@psi.ch >> http://sb.web.psi.ch >> **************************************** >> -- **************************************** Dirk Kostrewa Paul Scherrer Institut Biomolecular Research, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax: +41-56-310-5288 E-mail: dirk.kostrewa@psi.ch http://sb.web.psi.ch **************************************** CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 14 March 2007 |
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