Re: [modeller_usage] How to incorporate NAD and water in my model

["Charlie Allerston" <>]

> 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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