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Re: [modeller_usage] symmetry and molecular dynamics

We are trying to build a homotetramer model but having some difficulty maintaining symmetry. I've read the previous posts but maybe someone can help me further - I'm new to Modeller and to Python.

It's hard to tell from the code snippet. It looks correct (I'm assuming this code is from the special_restraints method?) but maybe you're not using the class properly elsewhere in the script - can you post your complete script? The most common mistake is to derive a 'mymodel' class from 'automodel' but then to instantiate a regular 'automodel' object rather than the new 'mymodel', in which case any additional restraints, patches etc. in 'mymodel' are not applied.

We can think of a few ways to get around this:
1) do no molecular dynamics, only minimisation (maybe someone can tell me how?)

Sure, you can set automodel.md_level to None, which will turn off the MD refinement part. But if MD is not maintaining the symmetry, it seems unlikely to me that CG minimization would. It is more likely that there's a problem with your energy function.

2) run molecular dynamics only on selected regions of the model so that the core remains fixed in place (again, how would I do this?)

Doesn't http://salilab.org/modeller/manual/node23.html do what you need here?

3) learn Python and write restraints using symmetry matrices (if someone has implemented something like this before I'd love to see their code!)

I personally haven't come across such a restraint, but if anybody has written one and wishes to contribute it, I'd recommend the Modeller wiki for this purpose.

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage