[Chimera-users] Fitting a structure to a DAMMIN/SAXS model/volume

Thomas Goddard goddard at cgl.ucsf.edu
Mon Jan 25 10:46:21 PST 2010

Hi Andy,

   I have not tried this but here are my ideas.

   First when you open the bead model (PDB file) it will probably look 
crazy because Chimera is trying to treat the bead model as a molecule 
when really it is just a grid of points.  It may try to draw a ribbon 
through it.  So hide the ribbon and show the atoms as spheres using menu 

	Actions / Ribbon / hide
	Actions / Atom / show
	Actions / Atom / sphere

or equivalent commands

	repr sphere

To fit a molecule into the bead model I suggest turning the bead model 
into a density map using the molmap command.  For example, if the bead 
model is #0, make a 20 Angstrom resolution map with

	molmap #0 20

This just puts a Gaussian at each bead position to make a density map.

Then place the molecule into this map in the suspected position by hand 
and locally optimize that fit with the Fit-in-Map tool.


A new Chimera feature in Chimera daily builds computes theoretical SAX 
profiles for a PDB model and plots them against experimental profiles.

	Tools / Higher-Order Structure / Small-Angle X-ray Profile

It uses a web service hosted at our lab to compute the profile.  It 
isn't yet documented (added just a few weeks ago).


> Chimera Team & users,
> We have been using SAXS data and the DAMMIN software from the Svergun group.
> The bead model that DAMMIN produces approximates the shape and volume of the molecule.
> If one has a three dimensional structure of the molecule, then it becomes valuable to
> do a best superposition of the structure into the bead-model shape.  Chimera is
> our preferred molecular display & analysis software, and we would like to perform
> this fitting in Chimera.  Do you have any experience in how to display the bead-model
> output of DAMMIN and to fit or superimpose the bead model with a known structure?
> Thanks
> Andy Byrd

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