[Chimera-users] minimization with nonstandard atoms

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 7 11:13:41 PST 2012

Hi Jon,
As you saw, Fe is not supported; only these ions are handled:
Na+, K+, Rb+, Cs+, Mg2+, Ca2+, Zn2+, and Cl–


One workaround is to first change the element Fe to one of the handled types, say Mg or Zn.  Ways to change element are: text-editing the PDB file, or using the Modify Structure section of Build Structure (under Tools...  Structure Editing), or using a command something like:

setattr a element Mg Fe

If there is concern this may change the structure, you can freeze the ion and nearby residues so that they don't move. You would do that by selecting a zone around the ion (Ctrl-click it and then use "Select... Zone..." in the menu) and specifying "Fixed atoms: selected" in the Minimize Structure  tool.  Of course, then that part of the structure won't be adjusted.

Another workaround is to simply ignore the HEM residue (including Fe) which bypasses assigning parameters to it.  This also freezes the ignored part.  This approach requires using the minimize command and its "fragment" option, only available in the command (not GUI), and in fairly recent builds of Chimera 1.6.  Example command:

min fragment true spec ~:hem nsteps 10 cgsteps 0 interval 2 

Description of minimize command and its options:

In my opinion, one should be aware that minimization has limited ability to improve complicated structures such as proteins (in contrast, it is excellent for cleaning up warped small molecules), and that you should keep your initial homology model for comparison.  Many homology modeling procedures already take steps to generate energetically reasonable structures, and minimization may provide little or no improvement over the initial model.  Besides for small molecules, I might use minimization to do local cleanup of structures after manual "docking" or bond rotations had generated strained bonds and/or clashing atoms.

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 Feb 7, 2012, at 9:00 AM, Jon N. Rumbley wrote:

> I was hoping to minimize a homology model containing two heme groups. To understand how I might do this I have been starting with the known structure 1a6m. As suggested in the documentation I begin with Dock Prep and calculate charges etc… To my surprise Chimera alpha version 1.6 (build 34702) actually assigned charges to the heme. The problem is with the minimization itself. Within Minimize Structure I turn off all of the Dock Prep steps and simply try to minimize the structure but get an error,”Element Fe (atom #0:154.A at FE) is not currently supported”. I was assuming the charge calc was going to be the hard part but now I am stuck at this subsequent step. Is there something I can do to get the heme atoms recognized or is this simply not possible?
> Thank you,
> Jon Rumbley

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