UCSF chimera or chimeraX versions both could do the alignment of multiple structures that also pop up the sequence alignment with secondary structures highlighted in different colors through Match Maker. Up-to six structures I have aligned.
Best regards Rajivgandhi Sundaram. On Wed, Apr 8, 2020, 11:09 PM Armando Albert <xalb...@iqfr.csic.es> wrote: > Thank you all, > I have done it with chimera. It does structural alignment and use it as a > template. Then, you can add sequences one after the other and align to this > template. > You can save this alignment in clustalw format and load it to ESPrit3 and > do a nice picture. > Armando > > > > El 8 abr 2020, a las 19:22, Guillaume Gaullier <guilla...@gaullier.org> > escribió: > > Hi Armando, > > This seems doable with ChimeraX: https://www.cgl.ucsf.edu/chimerax/ > > More specifically, its matchmaker command will align two structures and > print the corresponding sequence alignment: > https://www.cgl.ucsf.edu/chimerax/docs/user/commands/matchmaker.html > You can then save the sequence alignment to a file, and use it in your > favorite sequence alignment program along with the sequences for which you > don’t have a structure. > > This is one option among many, as pretty much every structure > visualization program can superimpose two similar structures (but I don’t > know how many of them make it as easy to save the sequence alignment). > > Hope this helps, > > Guillaume > > > On 8 Apr 2020, at 19:04, Armando Albert <xalb...@iqfr.csic.es> wrote: > > Dear all, > I want to align two structures and then, I want to align several sequences > to that structural alignment. > How can I do this? > Armando > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
