Just to point out that the CCP4 wrapper to SSM "superpose" allows you to specify residue ranges to consider - very useful for multi-domain proteins. See the -s switches in http://www.ccp4.ac.uk/dist/html/superpose.html
I'm not clear if this was your issue. Cheers Martyn -----Original Message----- From: CCP4 bulletin board on behalf of Tânia Oliveira Sent: Fri 3/28/2008 5:20 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] 3D structure based alignment Hello, I´m having a problem that I would like to know if someone could help me. I want to do a 3D structure based alignment of my protein with another one. The problem is that my protein has 2 domains, and the structure that I want to superimpose just have one. I can do the structure superimposition by hand, but I´m not being able to do the sequence alignment based on the 3D structure, because the program that I´m using (SSM) starts to superimpose the sequence of my second domain in the beginning of the sequence of my reference model (exactly the same thing that it does with the sequence of the first domain). Do you know if there is any program where I can do this. Thanks in advance, Tânia Oliveira, PhD Student Membrane Protein Crystallography and Microbial Biochemistry Laboratory - ITQB-UNL
