Jack Shultz wrote:
Good o know about those options. I was just skimming through section 2 in the manual over lunch and I came across this example script. Would this also work? If so, are there any advantages to using model-segment.py? [2.2.9 Using your own initial model]
Sure, that would also work, but in that case you'd have to first generate a PDB file as the initial model. In this case, since your target and template are 100% identical, the default initial model will match the template exactly anyway, so there seems little point in using your own initial model. The initial model is simply the starting guess for the optimizer - it doesn't otherwise affect the way in which models are constructed.
In homology modeling, the output models will not be exactly the same as the input (sidechain dihedrals will vary, for example). If this bothers you, you can fix the positions of some or all of the atoms you already know. That's the advantage of using model-segment.py.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage