[modeller_usage] missing residue build using automodel

[Mary Varughese <>]

Hi,

This is the align_multiple.ali file of automodel example,

C; A multiple alignment in the PIR format; used in tutorial

>P1;5fd1
structureX:5fd1:1    :A:106  :A:ferredoxin:Azotobacter vinelandii: 1.90: 0.19
AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELA
EVWPNITEKKDPLPDAEDWDGVKGKLQHLER*

>P1;1bqx
structureN:1bqx:   1 :A: 77  :A:ferredoxin:Bacillus schlegelii:-1.00:-1.00
AYVITEPCIGTKCASCVEVCPVDCIHEGEDQYYIDPDVCIDCGACEAVCPVSAIYHEDFVPEEWKSYIQKNRDFF
KK-----------------------------*

>P1;1fdx
sequence:1fdx:1    : :54   : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00
AYVINDSC--IACGACKPECPVNIIQGS--IYAIDADSCIDCGSCASVCPVGAPNPED-----------------
-------------------------------*

modelmultilple.py has this code;

a = automodel(env,
              alnfile  = 'align-multiple.ali', # alignment filename
              knowns   = ('5fd1', '1bqx'),     # codes of the templates
              sequence = '1fdx')               # code of the target

I dont understand this. I mean the real purpose of this code.
I thought 'sequence' is the target we want to achieve and it has no gaps. but here 1fdx has so many breaks. 
Could anyone tell me the real meaning of this alignment.

Thanking you
-- 
Mary Varughese
Research Scholar
School of Pure and Applied Physics
Mahatma Gandhi University
India