[Chimera-users] Constrainted fitting

Tom Goddard goddard at sonic.net
Wed Oct 23 16:32:21 PDT 2013


Hi Christoph,

  If I understand your question you have two PDB files of monomers that form a dimer and you want to fit them into a density map as a rigid unit without disturbing how they bind to each other.  This is easy to do in Chimera.  If you are using the Fit in Map dialog just select both monomers (e.g. command "select #1,2") then use the Fit "selected atoms" setting in the dialog.  This will move selected two monomers rigidly as one unit to the locally optimal position in the density map.  You can do this with a command instead of the fitting dialog "fit #1,2 #3".

	Tom


On Oct 22, 2013, at 4:37 AM, Christoph Wigge wrote:

> Dear all,
> 
> I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance.
> 
> Bests 
> 
> Christoph Wigge
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