Having indeed written Gesamt some 10-12 years ago, I had to refresh my memory before answering.
Gesamt definitely aligns multiple structures, just give them all on command line. It should do clustering in "sheaf" mode (which assumes that chains have same lengths and atoms are matched one-to-one). May be Daniel (in cc) can see how to implement clustering in his doings. Gesamt can also identify conformations, i.e. similar substructures with relative displacement or rotation in compared structures. Run gesamt without parameters to print all command-line options. For saying more I need specific questions. Eugene ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Armando Albert <xalb...@iqfr.csic.es> Sent: 06 March 2023 15:19 To: ccp4bb <ccp4bb@jiscmail.ac.uk> Subject: Re: [ccp4bb] Structural alignment and classification Thank you all. What about the analysis? Does any program cluster the structures according to their structural similarity? Armando > El 6 mar 2023, a las 15:58, Harry Powell > <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> escribió: > > Hi Eleanor > > According to > > https://www.ccp4.ac.uk/html/gesamt.html > > "Gesamt aligns two or more structures…” > > and > > https://www.ccp4.ac.uk/html/superpose.html > > "superpose aligns and superposes two or more protein structures…” > > But the real expert is probably Eugene. > > Harry > >> On 6 Mar 2023, at 14:55, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: >> >> Does Superpose or GESAMT align multiple structures? >> And can either read the NMR format and apply alignment to MODEL 1 ; MODE:L 2 >> etc? >> Eleanor >> >> On Mon, 6 Mar 2023 at 14:53, Harry Powell >> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >> Or you could use Gesamt - also in CCP4. >> >> Harry >> >>> On 6 Mar 2023, at 13:15, Kay Diederichs <kay.diederi...@uni-konstanz.de> >>> wrote: >>> >>> Dear Armando, >>> >>> besides THESEUS, you could use SUPERPOSE (in CCP4) or USalign >>> (https://zhanggroup.org/US-align/). >>> In my tests, THESEUS sometimes crashed in different ways. USalign is very >>> robust; SUPERPOSE is fast. >>> >>> HTH, >>> Kay >>> >>> On Mon, 6 Mar 2023 08:35:20 +0100, Armando Albert <xalb...@iqfr.csic.es> >>> wrote: >>> >>>> Dear all, >>>> I want to align several structures we obtained from a fragment screening >>>> campaign and cluster them according to RMSD. >>>> Is MNYFIT still running? What else can I run? >>>> Thank you >>>> Armando >>>> >>>> ######################################################################## >>>> >>>> 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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing >>>> list hosted by www.jiscmail.ac.uk<http://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 >>> >>> This message was issued to members of >>> www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list >>> hosted by www.jiscmail.ac.uk<http://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 >> >> This message was issued to members of >> www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list >> hosted by www.jiscmail.ac.uk<http://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 > > This message was issued to members of > www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list > hosted by www.jiscmail.ac.uk<http://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 This message was issued to members of www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://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 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/
