[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Re: [modeller_usage] How to incorporate NAD and water in my model
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
_________________________________________________________________
Solve the Conspiracy and win fantastic prizes.
http://www.theconspiracygame.co.uk/