[Chimera-users] Rotamer copying

[Ahir Pushpanath]

Hello there, I have a question regarding MODELLER in Chimera and the
ability of chimera to adjust the model using some inbuilt features
quickly(i.e. automatically, instead of interactively)

Firstly, I am trying to model the "holo" form of an enzyme with known
apo-form structure. I did this usinig the two independent domains of the
apo form as a template (in a bid to get the domains accurate) and for the
holo-form closure I used a very similar homologue that has been solved in
the holo form. The results were good and I got a decent model that had
closed up like the homolog.

However, I noticed that in the model a lot of the sidechains have not been
modelled with the right rotamer. This is odd, as I gave it the two
independent domains as a template, so it had all the information it needed
to get that perfectly right.

Either way, this means, I need to manually "copy" the rotamers from the apo
form onto the "holo model", which is time consuming. I know from the
homolog that only two or three residues in the active site change rotamer
upon apo-holo conformational change. So, I just want an easy way to edit
the rotamers in the holo-model to copy the rotamers of the apo-form for all
residues.

Is there an easy way to do this, is it possible to this with a script? I
have no idea how to script, mind you!

Ahir
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