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
--
Dr. Gianluca Ottolina
Istituto di Chimica del Riconoscimento Molecolare CNR
Via Mario Bianco 9, 20131 Milano Italy
phone 0039 02 285 000 21
fax 0039 02 285 000 36
email
web www.icrm.cnr.it