Yes - I wrote something long long ago called compar. It is still there..
you give it XYZIN1 and XYZIN2 and I think it lists all distances somewhere E [ed1@setsuko ~]$ compar <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> <html> <!-- CCP4 HTML LOGFILE --> <hr> <!--SUMMARY_END--></FONT></B> <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> <pre> ############################################################### ############################################################### ############################################################### ### CCP4 7.0.042: COMPAR version 7.0.042 : ## ############################################################### User: ed1 Run date: 3/ 7/2017 Run time: 13:36:49 Please reference: Collaborative Computational Project, Number 4. 2011. "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242. as well as any specific reference in the program write-up. <!--SUMMARY_END--></FONT></B> FORMATTED SCRATCH file opened on unit 7 <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> Logical name: CMPTMP, Filename: /tmp/ed1/compar_TMP.30038 <!--SUMMARY_END--></FONT></B> unknown-format file is being opened on unit 1 for INPUT. *** RWBROOK error: point code unit function *** 1 -4 1 MMDB_F_Open *** file : XYZIN1 *** reason : cannot open a file *** continue running, may crash ... <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> COMPAR: XYZOPEN: Error opening logical name XYZIN1 COMPAR: XYZOPEN: Error opening logical name XYZIN1 Times: User: 0.0s System: 0.0s Elapsed: 0:00 </pre> </html> <!--SUMMARY_END--></FONT></B> you give it XYZIN1 and XYZIN2 and I think it lists all distances.. E On 3 July 2017 at 13:16, James Foadi <james_fo...@yahoo.co.uk> 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 > <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 > > > > >
