Hi,<br><br><span style="color:rgb(102,0,204)">This is the align_multiple.ali file of automodel example,</span><br><br>C; A multiple alignment in the PIR format; used in tutorial<br><br>&gt;P1;5fd1<br>structureX:5fd1:1    :A:106  :A:ferredoxin:Azotobacter vinelandii: 1.90: 0.19<br>
AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELA<br>EVWPNITEKKDPLPDAEDWDGVKGKLQHLER*<br><br>&gt;P1;1bqx<br>structureN:1bqx:   1 :A: 77  :A:ferredoxin:Bacillus schlegelii:-1.00:-1.00<br>AYVITEPCIGTKCASCVEVCPVDCIHEGEDQYYIDPDVCIDCGACEAVCPVSAIYHEDFVPEEWKSYIQKNRDFF<br>
KK-----------------------------*<br><br>&gt;P1;1fdx<br>sequence:1fdx:1    : :54   : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00<br>AYVINDSC--IACGACKPECPVNIIQGS--IYAIDADSCIDCGSCASVCPVGAPNPED-----------------<br>-------------------------------*<br>
<br><span style="color:rgb(102,0,204)">modelmultilple.py has this code;</span><br><br>a = automodel(env,<br>              alnfile  = &#39;align-multiple.ali&#39;, # alignment filename<br>              knowns   = (&#39;5fd1&#39;, &#39;1bqx&#39;),     # codes of the templates<br>
              sequence = &#39;1fdx&#39;)               # code of the target<br><br><span style="color:rgb(0,0,102)">I dont understand this. I mean the real purpose of this code.</span><br style="color:rgb(0,0,102)"><span style="color:rgb(0,0,102)">I thought &#39;sequence&#39; is the target we want to achieve and it has no gaps. but here 1fdx has so many breaks. </span><br style="color:rgb(0,0,102)">
<span style="color:rgb(0,0,102)">Could anyone tell me the real meaning of this alignment.</span><br><br>Thanking you<br>-- <br>Mary Varughese<br>Research Scholar<br>School of Pure and Applied Physics<br>Mahatma Gandhi University<br>
India<br>