Dear Ansuman - I suspect Escet is what you're after:
http://webapps.embl-hamburg.de/escet/
It factors in coordinate accuracy into comparisons. Check out the
references for explanation.
On 24/06/2013 08:55, herman.schreu...@sanofi.com wrote:
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
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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
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