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