[Chimera-users] Rotamer copying

Eric Pettersen pett at cgl.ucsf.edu
Tue Feb 7 12:49:41 PST 2012

Don't make me blush!  :-)


On Feb 7, 2012, at 3:01 AM, Ahir Pushpanath wrote:

> It works like a charm! Absolute genius Eric! Fourth time I have a  
> question with brilliantly helpful answers from USCF.
> Thanks
> Ahir
> 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
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120207/1d5b6007/attachment.html>

More information about the Chimera-users mailing list