Hi James
If you have access to a Phenix installation then phenix.find_alt_orig_sym_mate does what you want in one go. It tries to position the two MR structures on the same origin and symmetry site like Csymmatch. Besides computing a score value indicating the quality of the match it also computes the RMSD between the two structures. This RMSD is computed with the sequence alignment generated by the SSM superpose program. So if one MR solution is wrong it would yield a rather large RMSD value. Robert On 03/07/2017 13:16, James Foadi wrote: > 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: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk > personal web page: http://www.jfoadi.me.uk > > On Monday, 3 July 2017, 11:59, Eleanor Dodson <eleanor.dod...@york.ac.uk> > 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 <stephane.duquer...@u-psud.fr> > 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 [1] -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234 Links: ------ [1] http://www.jfoadi.me.uk/
