Dear Troy,
> First, it seems like my raw sequence should be formatted so that MODELLER
> can read it. Since this is just a sequence with no corresponding structure
> shouldn't the second line of the sequence file just be:
>
> sequence:
>
Here is the sample sequence from the manual :
>P1;1fdx
sequence:1fdx: 1 : : 54 : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00
AYVINDSC--IACGACKPECPVNIIQGS--IYAIDADSCIDCGSCASVCPVGAPNPED*
For a sequence that you call 1dum of say 98 aa
line1 should be:
>P1;dum1
What you need in line 2 is just
structureM:dum1: 1: : 98: :dummy: extra terrestrial:0.0:0.0
<--optional parameters>
(structureM for model)
You can thus read in a complete sequence but build a model for only part
of the entire length.
The format is enhances PIR.
There are format converters that can write out a pir format sequence. You
can use ClustalX for this.
You then need to edit the protein name in line 1 and put in the information
in line 2.
Hope this helps,
Shoba
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