Dear Azat,

Yes, the program can read maximum 5 sequences as input at a time. Ok, now I'm trying to do multiple structure alignment. With only 2 structures as input, the alignment is really good, but it's failing with 3 or more. It's giving following message: "............... openf5___> file does not exist: /disk2/pdb/pdb.ent/List.ent (do not worry about this one)

Multiple dynamic programming alignment (MALIGN): Residue-residue metric : /usr2/people/deb/exec/modeller4/modlib//as1.sim.mat Gap introduction penalty: -600.0000 Gap extension penalty : -400.0000 Length of alignment : 556

malign3d_> Alignment: 1

# Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 1atu 1bbi 1hia # ====================================== 1 1.142 0.274 L 112 T 55 D 98 fit2xyz_E> number of equivalent positions < 3: 1 recover__> MODELLER_STATUS >= STOP_ON_ERROR: 1 1 ...................."

Hope this time I'm not doing the same mistake as before. Please help, Debashis. ------------------------------------------------------------------------------ ("`-''-/").___..--''"`-._ `6_ 6 ) `-. ( ).`-.__.`) Debashis Mukhopadhyay (_Y_.)' ._ ) `._ `. ``-..-' Research Fellow,C&MB Div., _..`--'_..-_/ /--'_.' ,' Saha Institute Of Nuclear Physics, (il).-'' (li).' ((!.-' 1/AF, Bidhannagar,Calcutta-700 064. India. deb@cmb2.saha.ernet.in ------------------------------------------------------------------------------