Dear Modeller user, as a newcomer I have some questions about the alignment. I use Modeller to find structure and sequence related to the target sequence as described in the chapter 1.71 of the manual (SEQUENCE_SEARCH). I obtained five new file ( .tmp; .ali; .pap; .log; and .mat) and as suggested I check for the Z-score and I find five sequence with the score more than 4. Now I would like to use these five sequence to do the alignment as suggested in the chapter 1.7.2. Is Modeller able to calculate the alignment? Yes, I think. Now the real question is how to do this alignment with ALIGN, ALIGN2D, MALIGN and MALIGN3D. I try the example reported in the manual but something is wrong and the calculation aborted all the time. Can you please post another easy example of TOP file for ALIGN and comment it; the example in chapter 2.4.14 is not clear to me. How do I use the ( .tmp; .ali; .pap; .log; and .mat) file that I obtained previously?

Thanx Gianluca