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 lab: +33 (0)1 45 68 82 66 fax: +33 (0)1 45 68 89 93 email: sduq...@pasteur.fr ---------------------------------------------------- ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ *De: *"James Foadi" <000009daa8ec3774-dmarc-requ...@jiscmail.ac.uk> *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: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk personal web page: http://www.jfoadi.me.uk
