[Chimera-users] Fitting a structure to a DAMMIN/SAXS model/volume
goddard at cgl.ucsf.edu
Mon Jan 25 10:46:21 PST 2010
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
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?
> Andy Byrd
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