Hi It occurred to me after I posted that you might be using the CCP4 eco-system in which case you might be using either Superpose or Gesamt for structure-based alignment.
Harry > On 11 Feb 2026, at 10:49, Guillaume Gaullier > <[email protected]> wrote: > > 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, a mailing > list hosted by 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 ######################################################################## 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/
