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[modeller_usage] MODELLER BASIC HELP

I am recently started working with modeller ... and I have queries about it :-

1) It's written in the manual that the sequences should be in PIR format .. but for the template sequence I am not getting the second line , about the structure ?? from where I can get it ??
and whats the actual way for obtaining PIR sequences and with the structure details required  as required for the template??

2)How to align the two sequences in PIR foramat .. since I aligned the sequences in FASTA format I am not getting the same structure given in the manual as an example ??

3) Where do I have to save the .pdb file of the template in modeller and the code that is given for homology modeling , there is nothing mentioned about the .pdb file being used ??


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