Hi Eleanor.You do the alignment if you are looking to measure the similarity of
two molecules after refinement or the similarity of two molecules in general.
When you do this, like you say, you have to carry out some sort of alignment,
i.e. you move one of the two structures so to have the highest degree of
overlapping with the other , without any constraint. This is what most of the
programs do (and after having done that they compute the RMSD). But I'm looking
for a program to measure the RMSD of two fixed (un-moved) structures; the
structures have already been moved (with the symmetry and unit cell origin
constrain) by CSYMMATCH. Does it make sense to you?
James
Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell Science and
Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email:
[email protected] alternative email: [email protected] personal
web page: http://www.jfoadi.me.uk
On Monday, 3 July 2017, 11:59, Eleanor Dodson <[email protected]>
wrote:
Dont understand your Q James..
You have to make sort of alignment to get the RMSD surely?
And csymmatch will just apply the symmetry and origin shifts needed for any
comparisonn?
E
On 3 July 2017 at 11:32, Stéphane Duquerroy <[email protected]>
wrote:
Hi James
LSQMAN can calculate the current RMSD between the 2 models (RMsd_calc mol1
range1 mol2 range2 [Ltarget])
Be careful it renames the chain names
Stephane
------------------------------ ---------------------
Duquerroy Stéphane
Structural Virology Unit - PASTEUR INSTITUTE
25 rue du Dr Roux, 75015 Paris, France
lab: +33 (0)1 45 68 82 66
fax: +33 (0)1 45 68 89 93
email: [email protected]
------------------------------ ----------------------
De: "James Foadi" <000009daa8ec3774-dmarc- [email protected]>
À:
Envoyé: Lundi 3 Juillet 2017 11:47:00
Objet: [ccp4bb] RMSD between unaligned structures
Dear ccp4 tribe,this might have been asked before, but I haven't paid enough
attention.
I'd like to measure the RMSD between two models after molecular replacement. I
can force the two models to overlap as much as possible within the symmetry and
origin-shift constraints (using CSYMMATCH). But I don't want the program that
compute RMSD to align the two structures. Can you suggest what I should use?
And, perhaps, what keywords I should adopt?
Many thanks, in advance.
James Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell
Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office
email: [email protected] alternative email: [email protected]
personal web page: http://www.jfoadi.me.uk
