Re: criteria for best template....after comparison of many structures

[Bozidar Yerkovich <>]

Title: Re: criteria for best template....after comparison of many structures

Hi Gowtham,

SEQUENCE_SEARCH command will produce output, e.g.:

   # CODE_1      CODE_2 LEN1 LEN2 NID   %ID   %ID    SCORE  SIGNI SIGNI2 SIGNI3
--------------------------------------------------------------------------------
   1 TvLDH      1bdmA    335  318 153  45.7  48.1  212557.   28.9 -999.0 -999.0
   2 TvLDH      1lldA    335  313 103  30.7  32.9  183190.   10.1 -999.0 -999.0
   3 TvLDH      1ceqA    335  304  95  28.4  31.3  179636.    9.2 -999.0 -999.0
   4 TvLDH      2hlpA    335  303  86  25.7  28.4  177791.    8.9 -999.0 -999.0
   5 TvLDH      1ldnA    335  316  91  27.2  28.8  180669.    7.4 -999.0 -999.0

Which you can use to select the best template. More info can be found in manual and in three tutorials on MODELLER web site, under User Manual pages...

Good luck,
Bozidar




> hello fellow modellers....
> im trying to automate modeller to model some 200 proteins. i could generate a
> script which selects the the group of template. and my compare.top compares 
> all
> these templates and produces the output file called compare.log.
> 
> BUT  I DONT know what criteria i should use to select the best template out of 
> the
> bunch.  i attached my
> 
> compare.top
> compare.log
> files with this mail.(as compar.tar)   ..can any one help me ......... what
> information  i should look in  LOG file to select best template(s). if it is
> dendrogram..... how to do it...
> 
> many thanx in advance
> gowtham
> graduate student
> ICGEB
> New Delhi
> INDIA
> 

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