[Chimera-users] Rotamer copying

Eric Pettersen pett at cgl.ucsf.edu
Mon Feb 6 11:55:54 PST 2012

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 Pettersen
                         UCSF Computer Graphics Lab

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
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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