Hello,
Like Harry said, difficult to advise without knowing how you performed the superimposition. But in case it is helpful, the matchmaker command from ChimeraX generally does a good job for me without even having to use non-default settings: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/matchmaker.html So I would recommend trying it. It's well documented, and the ChimeraX team is very reactive on their email list in case you have questions. Cheers, Guillaume ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Harry Powell <[email protected]> Sent: Wednesday, February 11, 2026 11:19:48 AM To: [email protected] Subject: Re: [ccp4bb] Query regarding the structure-based sequence alignment Hi It depends on the software you’re using for the alignment. Some does a “better” job than others (e.g. I’d expect a strictly sequence based alignment like Blast to do a “good” job, but I’ve seen occasional misalignments [that are obvious to the eye!] with some of the HMM-based software like HHAlign - I have no idea why this might happen because the group that produces HH-suite doesn’t appear to be active enough to address issues on their github; I know that many of the authors are no longer working on the project). So, my follow-up question would be “which software are you using for this?”. Harry > On 11 Feb 2026, at 05:27, Thripthi Shenoy > <[email protected]> wrote: > > Greetings to all, > > I am currently working on understanding the structure-based sequence > alignment of the crystal structure of NOXA BH3 domain and the complete > protein structure obtained from AlphaFold. According to my understanding, the > BH3 binding domain from the crystal structure should get aligned with the BH3 > domain in the entire protein structure. However, this is not the case and the > identical amino acids of the BH3 domains are not getting aligned. I would be > grateful to know if this is a correct approach to proceed with the structure > based protein alignment. > > Thanking you in advance > With regards, > Thripthi S. > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## 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/ VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ######################################################################## 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/
