Fitting a SASREF model and a X-ray structure

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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Nyshae
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Joined: 2015.11.03 14:38

Fitting a SASREF model and a X-ray structure

#1 Post by Nyshae » 2016.09.28 14:45

Hi all,

I am working with a dimeric protein which has two domains. I made an atomic model of domain A and another for domain B (from literature data and homologous structures). I have SAXS data on the dimeric protein. Using both, I got a nice SASREF build (for the dimer). I later on got crystals of this dimer. Unfortunately I can only "see" domain A parts (which is the central domain which dimerizes).

First, is it possible to fit/superimpose the SASREF build and the X-ray structure (even if partial) ?
Second, what program would you use to do that ?

Many thanks!

sasha
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Posts: 46
Joined: 2014.03.05 17:56

Re: Fitting a SASREF model and a X-ray structure

#2 Post by sasha » 2016.10.06 00:00

If I understood properly, you have two high-resolution models of your dimer, with the crystallographic model lacking one domain.
You should be able to superimpose them with PyMOL using the 'align' or 'cealign' commands, the structures will be superimposed based the common section.
Other programs like Chimera, Swiss PDB viever, VMD, etc should be able to do the same.

Best,

sasha

Nyshae
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Posts: 24
Joined: 2015.11.03 14:38

Re: Fitting a SASREF model and a X-ray structure

#3 Post by Nyshae » 2016.10.17 13:36

Thanks for your input!
I have basically one crystallographic model of my dimer where you can only see the dimeric interface of domain As and also computed atomic models of each domain A and B separately.
I am already using PyMOL to do that but I would have liked to get a program that could also issue a fit curve or a fit variable.
Cheers!

sasha
Active member
Posts: 46
Joined: 2014.03.05 17:56

Re: Fitting a SASREF model and a X-ray structure

#4 Post by sasha » 2016.11.23 15:09

Nyshae wrote:Thanks for your input!
I have basically one crystallographic model of my dimer where you can only see the dimeric interface of domain As and also computed atomic models of each domain A and B separately.
I am already using PyMOL to do that but I would have liked to get a program that could also issue a fit curve or a fit variable.
Cheers!
Hi there, I don't understand the problem, what exactly do you want to compare against what? You can superimpose each domain independently on the SASREF model, if that's what you need.
To compare high-resolution models against each other, the most popular measure would be RMSD.

To obtain a curve and goodnes-of-fit chi-square value, compare the high-resolution model to your SAXS data using the CRYSOL program. SASREF provides fit curve and chi-square as well while generating the model.

From PyMOL, you can run CRYSOL directly using the SASpy plugin distributed with ATSAS.

Best,

sasha

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