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 ======================================================================= Shoba Ranganathan, Ph D Tel:+61-2-9351-1870 ANGIS, Bay 16, Suite 104 Toll free:1-800-728-028 Australian Technology Park Fax:+61-2-9351-1878 Eveleigh NSW 1430 Australia Personal URL: http://molmod.angis.org.au/~shoba ================MolMod Home Page: http://molmod.angis.org.au===========