Dear sir I am new user of modeller. I modelled 3 targets using 4 tempelates. i used the MALIGN and GET-MODEL top files for modelling. but my protein has only 15-20% identity with the tempelates and after modelling when i visualised in "O" the loops and some conserved secondary structural elements are modelled incorrectly. It may happens due to wrong sequence alignement since very less in sequence identity. I compared my targets with the model which i got from MODWEB server, it shows that target got from MODWEB server(it used one tempelate)was better than targets i got from MODELLER7v7. i want to have as many as models to do MOLECULAR REPLACEMENT. Please could you suggest me how to edit sequence alignment and how to get best sequence alignement with the tempelates. Thanking you in advance. rajkumar CCMB INDIA
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