Dear Ansuman, It is not entirely clear to my what kind of answer you are expecting. As Tim mentioned, from the B-factor formula, one can derive an estimate of the deviations of atoms from their average positions. This should give some idea of the inherent flexibility of the protein. From my experience, I would consider RMS deviations of 0.2-0.3Å between protein loops not significant. However, movement of an atom of 0.2Å in the active site of an enzyme (e.g. with a transition state analog), especially when backed up with positive and negative difference electron density peaks, when the atom is forced in its original position, could be highly significant.
My 2 cts, Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Tim Gruene Gesendet: Sonntag, 23. Juni 2013 19:54 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] query regarding RMSD calculation -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear ansuman, 'rmsd' stands for 'root mean square deviation', i.e. in the context of your first question you must sum the _square_ of the atomwise deviations and then take the square root. question two: I contradict: residues ARE static in this context: a crystallographic structure model corresponds to the average of all asymmetric units in the crystal, hence the resulting coordinates represent an average value and therefore are to be considered static. The fact that we assume that between two asymmetric units certain deviations from the average will occur is modelled by the (isotropic / anisotropic) ADP and the occupancy, respectively, but nevertheless, the model that you use for calculating an rmsd is a static one. This may be the reason why there is not one answer to your question two, but may give rise to a longish discussion. Best, Tim On 06/23/2013 02:50 PM, ansuman biswas wrote: > Dear all, I have 2 queries regarding RMSD calculation and > interpretation. > > 1. When 2 residue stretches are superposed using CCP4 superpose, the > log file shows the atomwise-deviations between matched residue pairs. > How to find the total deviation/RMSD between a specified residue pair > - should the RMSDs of the individual atoms be summed over, or is there > some other formula? > > 2. Residues are not static; this dynamic nature is evident from > variations (for a given residue; by variations, I mean that the > residues don't superpose completely) when multiple chains of the same > structure (from multiple chains in AU of a PDB, or from different > PDBs) are superposed. My question is: is there an RMSD cut-off below > which the variation can be considered as thermal fluctutation, and > above which they can be said to be a different 'conformation' or > 'state'? > > Thanking all, regards, ansuman > - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRxzZMUxlJ7aRr7hoRAog8AKDistu4ryi4DMUjgHlxXNl0wLV48ACcD1PI OYiO3+oZTZ3RoBjNKY9GR/I= =zyHZ -----END PGP SIGNATURE-----