[Chimera-users] Chimera/Modeller to add missing residues

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 14 10:00:57 PST 2017


Forgot to finish this one thought, sorry...

> On Nov 14, 2017, at 9:47 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> An important point is that the Chimera-Modeller interface will only model one chain at a time.  It does not care that other chains are there, so any added residues/loops might end up clashing with the other chains.  In this case it didn’t seem

… that bad since the added residues were on the outside of the complex.  However, Find Clashes/Contacts (in menu under Tools… Structure Analysis) identified a few clashes between those chains and the other chains in the merged model in my test.  I only made one Modeller model of each chain.  One reason you might want to try making more than one model of each chain is that they may have different numbers of clashes with the other chains in the structure.  However, whether you care about this depends on what you are going to do with this overall structure. If it’s just for a picture, it’s not important, or if you were going to run minimization or dynamics, the clashes would easily resolve themselves in this case because they involve peptide termini on the outside of the complex.

Finally, if you want to use Modeller to model the multi-chain complex with awareness of the other chains, you would have to use it separately outside of Chimera.

Elaine


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