[Chimera-users] Addition of phosphates to PDB structures

Thu May 10 12:07:37 PDT 2012

Hi Elaine,

Thank you for your prompt reply; I will try your suggestions. Also, since you mentioned docking programs, which one would you suggest using in conjunction with Chimera specifically for the purpose of docking ATP into a known ATP binding site?

From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Wednesday, May 09, 2012 8:32 PM
To: Donado, Carlos
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Addition of phosphates to PDB structures

Hi Carlos,
How to add a phosphate group is discussed in this earlier post:


Chimera does not "dock" ligands into binding sites automatically.  If you are using only Chimera and not docking programs, probably the most reasonable way is to superimpose the protein with a related protein structure that does contain the ATP, then remove or hide (depending on what you want to do next) the related protein structure except for the ATP part.

It's easy to superimpose proteins using the MatchMaker tool (or mmaker command).  For details see the documentation,

General discussion of methods for superimposing structures:

Of course you could also open your protein and an ATP molecule as separate models and then try moving the ATP into the site by hand, possibly rotating some bonds of protein sidechains or in the ATP, but that is usually quite difficult.

How to "freeze" (deactivate) one structure so that only the other one moves:
How to rotate bonds:

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 9, 2012, at 4:34 PM, Donado, Carlos wrote:

> Hi all,
> I would like to learn how to add a phosphate group to a particular residue, resembling phosphorylation of a particular residue, to a PDB structure. If this is doable using Chimera I would really appreciate any hints on how to do this.
> Also, I am new to Chimera but I was wondering if there was a way of adding ATP to a designated ATP binding site.
> I would very much appreciate any responses,
> Thanks,
> Carlos Donado

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