>Charlie Allerston wrote: >>Do you have to use the modeller alignment script? I have been using ebi >>software to create a .pir file. > >No, you do not need to use Modeller to make your alignment file. However, >since there are no standard one-letter codes for ligands, you will likely >have to edit your original alignment in a text editor to put in the >ligands. >
This is what I am not getting. Where to put the ligand in the alignment, regardless of what character to use. Take this for instance. trying to model something from the template 1VDC http://www.rcsb.org/pdb/explore.do?structureId=1VDC Looking at the PDB file it has 316 residues then it had a molecule of FAD tacked on at a position designated 400. So when I align this to some target like below (cropped).
--------------------------MNGLETHNTRLCIVGSGPAAHTAAIYAARAELKP LLFEGWMANDIAPGGQLTTTTDVENFPGFPEGILGVELTDKFRKQSERFGTTIFTETVTK VDFSSKPFKLFTDS---KAILADAVILAIGAVAKRLSFVGSGEVLGGFWNRGISACAVCD GAAPIFRNKPLAVIGGGDSAMEEANFLTKYGSKVYIIHRRDAFRASKIMQQRALSNPKID VIWNSSVVEAYGDGERDVLGGLKVKNVVTGDVSDLKVSGLFFAIGHEPATKFLDGGVELD SDGYVVTKPGTTQTSVPGVFAAGDVQDKKYRQAITAAGTGCMAALDAEHYLQEIGSQEGK SD- * >P1;fake1
DASGLSVAAAATLSQKSTPYYQSEIHTIGKRRMHSKVVIIGSGPAAHTAAIYLARAELKP VLYEGFMANGVAAGGQLTTTTEVENFPGFPEAVTGQELMDKMRAQSERFGTVIVSETVGK LDLSKRPFEYSTEWSPDTVMTADAVILATGASARRLGLPGED----KYWQNGISACAVCD GAVPIFRNKPLVVIGGGDSAAEEAIFLTKYGSHVTVLVRRDKLRASSIMARRLLAN---- ------------------------------------------------------------ -------------KKVTGLFAAGDVQDKRYRQAITSAGTGCMAALDAEKYLEELEDEQAD GKL *
Where should I stick the fad? At the end? How many blk characters should I tack on? 1 because there is only one molecule? Is there a specific character for FAD?
These are my stumbling blocks.
regards
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