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Try POSA and FATCAT from Godzik group for structural clusters/trees and multiple/flexible structure alignments: https://academic.oup.com/nar/article/48/W1/W60/5848494 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086100/ https://posa.godziklab.org/ https://fatcat.godziklab.org/ Best regards, Debanu On Thu, Mar 9, 2023 at 3:57 PM Jon Cooper < [log in to unmask]> wrote: > Coot's ssm superposition does give the C-alpha rmsd, though, most easily > seen if you run it from a terminal window? I guess it can't be miles > different from a least-squares fit ;-? > > > Best wishes, Jon Cooper. [log in to unmask] > > Sent from Proton Mail mobile > > > > -------- Original Message -------- > On 9 Mar 2023, 13:55, Paul Emsley < [log in to unmask]> wrote: > > > On 06/03/2023 07:35, Armando Albert wrote: > I want to align several > structures we obtained from a fragment screening campaign and cluster them > according to RMSD. > To what end, may I ask? I would use LSQKAB, parse the > log files for the RMSD and create an input file for R. (One cannot just do > this in Coot, because, for LSQ fitting, Coot only returns the > transformation matrix, not any fitting statistics - in retrospect this is > obviously an oversight.) Paul. > ######################################################################## To > unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This > message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > -- --- LinkedIn: www.linkedin.com/in/debanudas Cal Alumni: cal.berkeley.edu/debanudas ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/