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
On 6/23/12 2:27 AM, Mary Varughese wrote: > I thought 'sequence' is the target we want to achieve
That's correct.
> and it has no gaps. but here 1fdx has so many breaks.
No, all Modeller cares about is which residue(s) in the template(s) are aligned with each residue in your target sequence. You can add gaps as necessary to make this easier (for example, if you don't want to use some residues in your template, you can add gaps to the target rather than having to edit the PDB file to remove those residues). Gaps only affect the alignment - the final 3D model doesn't contain any gaps (if you want "gaps" in the 3D model, add chain breaks - "/" characters - to the alignment).
Ben Webb, Modeller Caretaker
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Mary Varughese -
Modeller Caretaker