I second the use of LSQMAN.
The command for calculating wo aligning appears to be:
rmsd_calc (abbreviated rm).
http://xray.bmc.uu.se/usf/lsqman_man.html#S59
If you have multiple chains, use the option "chain_mode original"
before loading the pdb's to avoid renaming chains:
http://xray.bmc.uu.se/usf/lsqman_man.html#S25
On 07/03/2017 06:32 AM, Stéphane Duquerroy 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
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>
> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> *De: *"James Foadi" <[log in to unmask]>
> *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: [log in to unmask] alternative email: [log in to unmask] personal web page: http://www.jfoadi.me.uk
>
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