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Again MALIGN



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.
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  ("`-''-/").___..--''"`-._			
   `6_ 6  )   `-.  (     ).`-.__.`)	     Debashis Mukhopadhyay
   (_Y_.)'  ._   )  `._ `. ``-..-'	     Research Fellow,C&MB Div.,
 _..`--'_..-_/  /--'_.' ,'                   Saha Institute Of Nuclear Physics,
(il).-''  (li).'  ((!.-'                     1/AF, Bidhannagar,Calcutta-700 064.
                                             India.
                                             
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