[Chimera-users] Rotamer copying

Ahir Pushpanath ahir29 at googlemail.com
Tue Feb 7 03:01:51 PST 2012

It works like a charm! Absolute genius Eric! Fourth time I have a question
with brilliantly helpful answers from USCF.


On Mon, Feb 6, 2012 at 7:55 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> I have attached a script that, if you have exactly two models open and
> they have the same residues, will copy the chi angles of the lower-numbered
> model into the higher-numbered model.  You can run the script simply by
> opening it with File->Open.
> --Eric
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
> On Feb 6, 2012, at 10:51 AM, Ahir Pushpanath wrote:
> 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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