Search found 346 matches

by SaxsMax
2013.06.10 14:10
Forum: Rigid Body Modelling
Topic: CORAL unzipping error?
Replies: 2
Views: 2594

Re: CORAL unzipping error?

Sure, please download
unzip.exe from the "addon" subfolder of the ATSAS 2.5.1 download page (where dbloop.zip is also located)
http://www.embl-hamburg.de/biosaxs/atsa ... wnload.php
and put it in Atsas installation folder or anywhere else on the system path.
by SaxsMax
2013.04.19 16:51
Forum: Rigid Body Modelling
Topic: Protein-heparin complex using Coral
Replies: 3
Views: 2297

Re: Protein-heparin complex using Coral

Ideally, the ones which are expected to be on the interface with the protein
by SaxsMax
2013.04.19 09:08
Forum: Rigid Body Modelling
Topic: Protein-heparin complex using Coral
Replies: 3
Views: 2297

Re: Protein-heparin complex using Coral

Is the binding site for heparin is known? Or may be even the structure of a domain with bound heparin? If latter is the case then one can use such a model as one rigid body in either Coral or Bunch. If however heparin has to be a separate rigid body, then only Coral can be applied. Also in this case...
by SaxsMax
2013.03.27 20:35
Forum: Ab Initio Shape Determination
Topic: DAMMIN having worse fits than GNOM
Replies: 5
Views: 3274

Re: DAMMIN having worse fits than GNOM

The presence of detergent is to my mind the source of the problems with ab initio modelling from this data.

Also, the experimental errors are missing (zeroed) which affects the Gnom analysis.
by SaxsMax
2013.03.26 11:29
Forum: Ab Initio Shape Determination
Topic: DAMMIN having worse fits than GNOM
Replies: 5
Views: 3274

Re: DAMMIN having worse fits than GNOM

Would you mind posting also the original data, i.e. not processed by Gnom? Where was it measured? At a synchrotron or on a lab source? In the latter case the data is probably smeared. Were several concentrations measured, is there any concentration effect? Also, is the sample just a protein or a pro...
by SaxsMax
2013.03.19 17:33
Forum: ATSAS Package in General
Topic: ATSAS release 2.5.1
Replies: 4
Views: 5879

ATSAS release 2.5.1

Dear Small-Angle Scatterers, This message is to announce a new ATSAS bug-fix release 2.5.1 Changes in programs ------------------- * almerge: improved handling of file properties, merge two files, extrapolate if more than two * autorg: writes error messages to stderr, improvements in computation of ...
by SaxsMax
2013.02.27 16:55
Forum: Working with Models
Topic: cryson and gnuplot
Replies: 1
Views: 2152

Re: cryson and gnuplot

As the format of Gnuplot commands change between the Gnuplot releases, it was decided not to support Gnuplot graphics inside Crysol/Cryson anymore. Still, QuickWin versions of both programs allow one to visualize the obtained fit. UPD: Please disregard the above info. In Crysol, apparently the Gnup...
by SaxsMax
2013.01.25 17:29
Forum: Rigid Body Modelling
Topic: SASREF06 vs SASREF07
Replies: 5
Views: 4535

Re: SASREF06 vs SASREF07

Crysol in its present form also has its limitations. Particularly, for elongated/skewed particles as well as for the shapes with the cavities, envelope function evaluated on Fibonacci grid would not present the hydration shell very accurate. A new Crysol version is actually planned for the next Atsa...
by SaxsMax
2013.01.25 14:54
Forum: Rigid Body Modelling
Topic: SASREF06 vs SASREF07
Replies: 5
Views: 4535

Re: SASREF06 vs SASREF07

Sasref7 additionally adjusts a background constant while Sasref6 does not. That is why the former typically yields better fits. Difference between Sasref and Crysol is in shell evaluation: in Sasref(s) each individual subunit is surrounded by the shell, in Crysol the shell is evaluated for the molec...
by SaxsMax
2013.01.25 14:41
Forum: Ab Initio Shape Determination
Topic: MONSA: density of DNA
Replies: 1
Views: 1843

Re: MONSA: density of DNA

When fitting the X-ray curve
1.0 for protein and 2.0 for nucleic acid are reasonable.

In case of SANS the provided densities should correspond to
the contrast of the phase at the given conditions (D2O in solvent, perdeuteration level)
by SaxsMax
2013.01.25 14:38
Forum: Ab Initio Shape Determination
Topic: inversion centre in dammin
Replies: 1
Views: 1677

Re: inversion centre in dammin

Though Dammin is applicable to various isotropic systems, it is primarily oriented to biological samples
and therefore there is no option for inversion centre symmetry
by SaxsMax
2013.01.25 14:34
Forum: Working with Models
Topic: How to change default CRYSOL solvent?
Replies: 1
Views: 2544

Re: How to change default CRYSOL solvent?

Crysol allows one to specify the electron density of the solvent.
Default is 0.334 e/A^3 which corresponds to the water
by SaxsMax
2013.01.25 14:22
Forum: Primary Data Processing
Topic: MW calculation with Autoporod
Replies: 1
Views: 1951

Re: MW calculation with Autoporod

The accuracy of MW estimate from the Porod volume is in fact about 20%
So do not worry about the mismatch, if the other types of analysis are compatible with the xtal structure
by SaxsMax
2013.01.25 14:19
Forum: Ab Initio Shape Determination
Topic: Is it reasonable to obtain Chi value lower than 1?
Replies: 1
Views: 2409

Re: Is it reasonable to obtain Chi value lower than 1?

If the experimental errors would be estimated absolutely correctly, the ideal model would give the chi value of 1.0 In practice, the error level is often under or overestimated (as in this particular case), therefore the obtained chi values might be less than one. Generally, the lower the chi is the...
by SaxsMax
2013.01.25 14:16
Forum: Working with Models
Topic: Crysol scattering curve in vacuum
Replies: 1
Views: 2819

Re: Crysol scattering curve in vacuum

Does Crysol evaluates the envelope function only to have a reference grid to make the hydration layer, or is there any other purpose? Envelope function is used only for the evaluation of hydration shell (and its scattering). There are Five columns in *.int ASCII file made by Crysol: (1) experimenta...