is it correct to perform homolgy modelling of a particular length of fasta sequence rather complete fasta sequence?
Correct/Incorrect status of model depending upon the choice of protein sequence of your interest and which type of structural information u can try to extract from model? generally entire protein sequence is important for alignment between target and template. if alignment score is significant, then go ahead for 3D structure prediction using homology modeling.
if your entire protein sequence is important for structure and function, then u need to take entire sequence for homology modeling else it show lack of structural integrity in predicted 3D model.
Any particular reason why you want to homology model of a part sequence rather than the whole sequence?
its becoz the rest part of fasta sequence does not have suitable template to make model while the other for which it is available has been found to be crucial in its activity. thats y need to do homology modelling. so is it correct...?
it is technically incorrect. according to your data, u can use online servers depends upon fold recognition (Threading) method for molecular modeling i.e. Phyre or I-Tasser.
You can try ab initio modelling of the whole sequence. This method might work well in your situation where a suitable template is not found. Again may I ask you, the part which is important for crucial function, is it a protein domain ? If yes you might try Prodom or Pfam or GTOP to manually locate templates.
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