Well LSQKAB is set up to do this. You ask (not sure of the key words - always use gui or coot..)
FIT CA 7 15 chain A match CA 21 29 CHAIN B then you can add more spans as required .. You can do it in COOT Calculate LSQKAB - then select which residues to fit or from GUI1 However both LSQKAB LSQMAN will try to optimise the fit for the selected span. Do you want to fit 50 residues then get the error for just a few? LSQKAB will print out a table of all the fit distances, and give an overall RMSD, but you would have to select and average the span you want by some other means.. I think the same is true for LSQMAN Eleanor On Tue, 17 Sep 2019 at 16:07, Martyn Winn - UKRI STFC < [email protected]> wrote: > This is probably a good opportunity to say that the USF has moved to > https://github.com/martynwinn/Uppsala-Software-Factory > > Gerard asked for this so that they wouldn't be lost. I haven't put any > effort into checking the binaries or compilation, but I will do what I can > on a best effort basis ... > > Others are welcome to contribute ... > > cheers > m > > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > Degano Massimo > Sent: 17 September 2019 15:35 > To: ccp4bb > Subject: Re: [ccp4bb] Calculating RMSD of a loop > > Hi, > > (good old) LSQMAN from the Uppsala Software Facotry will do this for you. > First you align the structures based on the subset of atoms you want to > match, then use the RMSD command to calculate the rmsd for the subset of > atoms you are interested in. > Best wishes, > > Massimo > > -- > Dr. Massimo Degano > Biocrystallography Unit > Dept. of Immunology, Transplantation, and Infectious Diseases > IRCCS Scientific Institute San Raffaele > via Olgettina 58 > 20132 Milan - Italy > email: [email protected]<mailto:[email protected]> > phone: +39-0226437152 > fax: +39-0226434153 > skype: maxdegano > ORCID: 0000-0002-0787-1883 > > http://research.hsr.it/en/divisions/immunology-transplantation-and-infectious-diseases/biocrystallography.html > < > http://research.hsr.it/en/divisions/immunology-transplantation-and-infectious-diseases/biocrystallography.html > > > > > On 17 Sep 2019, at 15:31, Kyle Gregory < > [email protected]<mailto: > [email protected]>> wrote: > > Hi all, > > What is the best/easiest way to calculate RMSD of a loop for 2 c-alpha > aligned structures? > Thought I could do this in Coot but I only see this if I align the > specific loops, which I don't want to do. > > Thanks, > > Kyle > > ________________________________ > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > [5xmille]< > http://www.5xmille.org/?utm_source=mail&utm_medium=web_link&utm_campaign=5xmille_2018 > > > > 5xmille. INSIEME POSSIAMO continuare a scoprire nuove cure. > > CODICE FISCALE 07636600962 > > > Rispetta l'ambiente: non stampare questa mail se non รจ necessario. > Respect the environment: print this email only if necessary. > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
