[Chimera-users] Rotamer copying- Specific Residues only

[Eric Pettersen]

On Feb 8, 2012, at 8:27 AM, Ahir Pushpanath wrote:

> Eric, although the script is highly useful for what I previously  
> asked, I have come to the realisation that simply copying all the  
> apo chi angles to the holo form may not be ideal for me in this  
> particular situation. I noted that of around 200 residues modelled,  
> around 90 of them are modelled different to the apo, the rest are  
> modelled similar to the apo form. Of these 90, only around half are  
> truly changed in the holo form(literature evidence from homolog),  
> therefore I do require a script that is able to accept an input of  
> which residues to copy the chi angles for, I think this will be  
> useful for other users who want to copy chi angles from apo-holo  
> forms and other applications, and probably could be included in  
> later build versions of chimera, under structure editing.
>
> Do you think you could help me with this? I am only learning python  
> now, so my scripting is not at a good level for these types of things.

I've attached a modified script that will only copy the chi angles for  
residues that are selected in the lowered-numbered model.  It's up to  
you to select them somehow. :-)

> On another note, do you have any experience with using chimera to  
> model apo-holo transitions any other way without using Modeller?

I don't.  Maybe others on the list will have suggestions... ?

> Also, does chimera have the ability to do docking of ligands, i.e.  
> given you know the apo crystal structure, can you tell it to dock a  
> ligand and change conformation of protein,(similar to autodock)?

Currently Chimera cannot dock ligands.  If our next 5 years of funding  
gets approved by the NIH, we have proposed interfacing Chimera to an  
Autodock Vina web service that would allow docking to be carried out  
directly from Chimera.  Right now all you can do is prepare the input  
for / analyze the output of external docking programs in Chimera

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu



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