I am working on SNP. This is my first approach towards bioinformatics, so I am learning with each step and finding problems as well. After predicting functional SNPs, I am trying to see their direct effect on protein structure. As my protein structure was not available on PDB, I modeled it by GalaxyWEB (SWISS-MODEL is not giving the whole structure, i-tasser & Phyre2 produced low-quality structure- maybe because good templates are not available). Now I have produced the mutant structure by Scwrl4 ( as many people suggested it gives the best side-chain conformation prediction). Now, what should I do with these- should I check only RMSD, TM score and come to the conclusion? Actually I wanted to see more detailed in structural change caused by the deleterious mutations.