Search found 101 matches

by Hayds
2010.11.29 23:38
Forum: Primary Data Processing
Topic: Buffer Subtraction
Replies: 9
Views: 7133

Hi Mac, you can do this but you need to be very careful. Have a close look at the low angular range and make sure the buffer signal does not have higher intensity than the sample. I have found in a number of cases that I can adjust the buffer by more closely matching the high angle data (trying to k...
by Hayds
2010.11.25 23:09
Forum: Mixtures and Flexible Systems
Topic: Refining dummy atom positions
Replies: 4
Views: 4099

Hi, why not use BUNCH and symmetry to generate the oligomer? You can also use the more recently developed program CORAL (in the latest ATSAS package). I'm not sure why you need to use EOM? EOM should be used to assess flexibility and the degree of compaction of the construct, the models are only par...
by Hayds
2010.11.25 22:57
Forum: Working with Models
Topic: Damsup gives only NSD=0.000
Replies: 4
Views: 3526

Hi Esther,

this sounds like a paths problem. Can you post the output of the command damaver /a?

Cheers,

Haydyn
by Hayds
2010.11.25 10:51
Forum: Rigid Body Modelling
Topic: Restraints in SASREF
Replies: 3
Views: 4039

Hi Art, you should be able to use the following in your contacts.cnd file: drng 10 12 1 15 15 2 45 45 where drng defines a distance-range for the contacts and in this case the range is between 10 and 12 angstroms, between CA of residue 15 of subunit 1 and CA 45 of subunit 2. Give it a try and let us...
by Hayds
2010.11.24 21:25
Forum: Ab Initio Shape Determination
Topic: help with Gasbor
Replies: 10
Views: 6301

Hi RBelen, the fit is definitely better, but the P(r) function contains this extra feature which normally indicates significant inter-particle interaction or aggregation. Maybe you can cut a few more points and see if this feature goes away? You can normally get away with this provided not too many ...
by Hayds
2010.11.24 12:39
Forum: Ab Initio Shape Determination
Topic: help with Gasbor
Replies: 10
Views: 6301

Hi RBelen, in the GNOM .out file it looks like the Dmax is underestimated (in both the fit to the data and also in the p(r) function). Increase Dmax until the fit to the data at low angles is better and see if the p(r) function is till smooth and nicely decays to zero. If it does you should get bett...
by Hayds
2010.11.22 19:28
Forum: Ab Initio Shape Determination
Topic: Dammif & crysol
Replies: 8
Views: 6842

CRYSOL is designed to evaluate the scattering from macromolecules with known atomic (high resolution) structure (and fit it to experimental data); it is incorrect to use it on dummy atom models Yep, that's true. We have a utility called pdb2alm for this. Al, is it in the downloadable ATSAS 2.4 pack...
by Hayds
2010.11.22 10:03
Forum: Ab Initio Shape Determination
Topic: Dammif & crysol
Replies: 8
Views: 6842

Hi Lauren,

It's hard for me to say unless I see the data and the P(r) function. Is it possible to post the saxs profile, p(r) function and .fit/.fir files? You can always PM me if this is a problem.

Cheers,

Haydyn
by Hayds
2010.11.21 10:21
Forum: Ab Initio Shape Determination
Topic: Dammif & crysol
Replies: 8
Views: 6842

Hi Lauren,

in the .fit file you see the regularised curve from GNOM and the fit to this from the model. The fit to the actual SAXS data is shown in the .fir file. Does this look more like the fit you get when using CRYSOL and one of your models?

Cheers,

Haydyn
by Hayds
2010.11.19 20:54
Forum: Rigid Body Modelling
Topic: Does anyone have an atomic ruler?
Replies: 5
Views: 4187

Hi Mr Chips! The way I do this is to determine the center of mass of the rigid bodies (individually, ie. the starting subunits, not the final structure), then locate the nearest CA. I then use this as an identifier and calculate distances between the approximate centers of mass of the domains in the...
by Hayds
2010.11.19 18:48
Forum: Mixtures and Flexible Systems
Topic: EOM - plot of pool and resulting Rg distribution
Replies: 2
Views: 3395

Hi Katrine, Alex is right, both Pool and Selected data are in the Rg_distrxxx and listxx_ files. eg. Average Radius of gyration = 39.91 Histogram Radius of gyration = 39.71 Pool Average Radius of gyration = 42.36 Pool Histogram Radius of gyration = 42.07 Rg Pool freq. Sel. freq. 28.29 0.0000000000 0...
by Hayds
2010.11.17 19:24
Forum: Primary Data Processing
Topic: New to Data Processing
Replies: 2
Views: 2273

Hi Jtswinde,

we need a little more information about your specific problem to be able to help.

The new updated manuals are online now and can be found here:

http://www.embl-hamburg.de/biosaxs/software.html

Maybe this helps to get you started?

Cheers,

Haydyn
by Hayds
2010.11.16 19:08
Forum: Primary Data Processing
Topic: Interpretation of differences between scattering curves
Replies: 5
Views: 3700

No problem,

best of luck with your analyses!

:)

h
by Hayds
2010.11.16 15:19
Forum: Primary Data Processing
Topic: Interpretation of differences between scattering curves
Replies: 5
Views: 3700

Hi Chiara, it looks as if the model systematically deviates from the SAXS data in all three cases, although the overall dimension is about right. What region did you use for scaling the overlay (assuming they were scaled)? There is a hint that the green curve describes a larger particle than the oth...
by Hayds
2010.11.16 10:13
Forum: Primary Data Processing
Topic: Interpretation of differences between scattering curves
Replies: 5
Views: 3700

Hi Chiara, when you overlay the curves do they differ at any point? I am tempted to say that no reliable conformation change has been detected, as I see no obvious deviations in the curves. It is hard to detect small changes upon ligand binding, it is much easier when a large change occurs that impa...