Andy,
There may be a better answer but depending on the length of the gaps where structure information is lacking, you could use 2D structure prediction programs for those regions and then impose certain restraints on Modeller. For example, the last 10 residues in my protein of interest did not have anything to align with in the sequences of the 4 templates. Using 2D structure predictions (I used EVA to choose the best performing programs: http://salilab.org/~eva/sec/res_sec.html), it was noted that this was most likely a helical structure, and I then used restraints suggesting to Modeller to use this type of structure for this part of the protein. Otherwise, without the restraints, I got various structural possibilities for the Cterm.
In your case, you also have the alignment, so that should make it easier.
Hope this can help or that someone else will have a better idea.
-Charlotte Habegger-Polomat
Andy Arvai wrote:
>Hi, > >I'm a new user to modeller and I would like to do a sequence alignment >to a known structure which has gaps in the pdb file. The alignment >works with align2d, however the sequence of the missing residues in the >pdb file is not used. Ideally I would like to use the pdb file and the >full sequence (including the residues which are missing in the pdb >file). I know I can do an alignment of two sequences, but I'm wondering >if it would be possible to get the best of both worlds - using sequence >and structural information from the pdb file and also sequence >information from the missing gaps. I've tried putting the entire >sequence at the start of the pdb file with the SEQRES pdb keyword, but >this seems to be ignored. Thanks for any help. > >Andy > >_______________________________________________ >modeller_usage mailing list >modeller_usage@salilab.org >http://salilab.org/mailman/listinfo/modeller_usage > > >