Respected sir
Could you please clarify my doubt that among these four values which one we have to more preference (RMSD(Å),Seq.Id.%)'Eq.Pos.P-value) for selecting these four Structure's(2mdh:A,2mdh:B.1b8p:A,1dbm:A) for given example of advance modelling in modeller tutorial.
Really sorry for asking this same question again and again because i could not convince with your last messages and i hope this time you will clear my doubt.
thanks you somuch for your reply's
-----------------------------------------------------------------------------Multiple templates
The structure of the Malate Dehydrogenase 1bdm has been clustered in the DBAli database within the family fm00495 of 4 members (2mdh:A, 2mdh:B. 1b8p:Aand 1dbm:A). The multiple alignment generated by the command salign() in MODELLER is used in DBAli to generate a multiple structure alignment of the family. The alignment can be downloaded from the DBAli database or you can use the file `salign.py' to calculate it on your computer. -----------------------------------------------------------------------------
On 07/28/2012 01:51 AM, vmahesh@ibab.ac.in wrote: > Could you please clarify my doubt that among these four values which > one we have to more preference (RMSD(Å),Seq.Id.%)'Eq.Pos.P-value) for > selecting these four Structure's(2mdh:A,2mdh:B.1b8p:A,1dbm:A) for > given example of advance modelling in modeller tutorial.
There is no one measure which will always tell you the "right" template, since this depends on what you want to use the final model for, and which region of the model (e.g. an active site) is of most interest.
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
vmahesh＠ibab.ac.in