sasref7mx.exe

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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james2009
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sasref7mx.exe

#1 Post by james2009 » 2011.08.29 10:01

Hi,

Could some-one explain the main differences between SASREF ver7 and SASREF ver7mx? Is this the new version of SASREF we should use, or a beta?

When you run it, the header says, "MIX version: a fraction of an extra component can contribute to all the curves"

I was trying to work out exactly what this means. Do you mean e.g. a small molecule like ATP?

Thank,

James

Alex
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#2 Post by Alex » 2011.09.05 11:44

Hi

This is a new version of SASREF (Ms in preparation), which accounts for possible oligomeric mixture. For example, you are modeling dimer with P2 symmetry, but there can be a fraction of monomers contributing to scattering curve.

Alex

tdgrant1
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#3 Post by tdgrant1 » 2011.09.06 20:27

Can I ask where you found this sasref7mx? I checked my Windows, Mac, and Linux installs and didn't see it (all latest releases).

Alex
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#4 Post by Alex » 2011.09.07 11:34

Hi,

I installed ATSAS two days ago on windows machine and it is there. I think
it is already in typical installation, but to be on the safe side you can
choose complete installation

Alex

tdgrant1
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#5 Post by tdgrant1 » 2011.09.07 15:22

Hmm, I did a complete install yesterday with the latest version for Windows 7 64-bit and it wasn't there, or at least I couldn't find it in C:\ATSAS. Did you install the XP 32-bit version by chance? I wonder if it's in the one but not the other.

franke
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#6 Post by franke » 2011.09.07 15:39

tdgrant1 wrote:Hmm, I did a complete install yesterday with the latest version for Windows 7 64-bit and it wasn't there, or at least I couldn't find it in C:\ATSAS. Did you install the XP 32-bit version by chance? I wonder if it's in the one but not the other.
The Windows7 package is still somewhat experimental and may not include all binaries the WinXP package has. We don't have enough Win7 users here for extensive testing (none to be exact) - sry.

tdgrant1
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#7 Post by tdgrant1 » 2011.09.07 15:42

No problem. I'll just use the XP one. Thanks!

tdgrant1
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#8 Post by tdgrant1 » 2011.09.07 18:34

I've installed the XP version and indeed sasref7mx is present there.

I'm interested in it because it seems to be the only program that may reveal the complex we are interested in. We have a monomer-dimer equilibrium where the dimer is a heterodimeric complex between two different components. We haven't been able to get the complex because even after gel filtration there is a concentration independent equilibrium, but it seems like sasref7mx is the program to help us.

However I'm a little confused as to how to use this program. The help file says
Such an additional component is described by an extra line at the end
of curves configuration file (with an arbitrary "dummy" name of the curve)
and of the cross-table file (both files are described in SASREF7 manual).
We only have one X-ray scattering profile, and the crystal structure of both monomers. What would the "extra line" at the end of these files be to include contributions from the monomer? Would it be simulated scattering from the monomer? I wouldn't think that necessary since sasref already calculates that for you, but maybe for including a "dummy" name?

Thanks for any help!

SaxsMax
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#9 Post by SaxsMax » 2011.09.13 18:39

Assuming that you have "a.pdb", "b.pdb" and "abmix.dat", the configuration files would be something along these lines:

curves.con:

Code: Select all

2
abmix.dat -1.0 P1 1 1.0 0 1.00 y
abmix.dat -1.0 P1 1 1.0 0 1.00 y
subunits.con:

Code: Select all

2
a.pdb y n P1
b.pdb y n P1
table.con:

Code: Select all

0.0 0.0
1.0 1.0
As one may probably see, the "subunits.con" here is the same as would be for a conventional Sasref7, the "curve.con" contains one extra line,
which corresponds to the scattering of dissociation product(s),
whereby the file name in this last line is just a dummy argument and what is really needed from this line is the symmetry.
Accordingly, an extra line is also present in the "table.con" which says that the dissociation products here are "a.pdb" and "b.pdb" in 1:1 ratio.

HTH

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