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Re: [IMP-users] Ambiguous restraints



Dear Francesco,

Ambiguity due to multiple copies of the same molecule is automatically taken into account.
The complement example use an obsolete interface, you should look into this tutorial:

https://github.com/salilab/imp_tutorial

cheers

Riccardo


Riccardo Pellarin, PhD
===================
Institut Pasteur
CNRS UMR 3528
25, rue du Docteur Roux
75724 Paris Cedex 15France


On Tue, Oct 29, 2019 at 4:13 PM Francesco RAIMONDI <">> wrote:
Dear all,

I have a set of MS/XL restraints which I'd like to use to predict the structure of a putative homodimeric protein. Some of the XL are expected to happen within the same chain, others between the two distinct chains of the homodimer.
The way I tackled the ambiguity issue so far is to explicitly generate all the possible XL/chain combinations and use this expanded list as an input for an adapted version of the human complement modeling script (https://salilab.org/Complement) using IMP v2.9.
Is there a better way to deal with ambiguity in IMP? I also found the AmbiguousCompositeRestraint class, but didn't yet manage to find an example script using it.
I'd be grateful for any suggestions you could provide me in this respect.

Thanks so much and all the best,
Francesco
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