Search found 788 matches

by AL
2024.06.04 12:44
Forum: Announcements
Topic: 2024 PhD school on SAS: principles, data analysis and advanced modeling
Replies: 0
Views: 62

2024 PhD school on SAS: principles, data analysis and advanced modeling

Small-angle scattering: Principles, data analysis and advanced modeling 18 - 23 August 2024 Copenhagen, Denmark The new PhD school on small-angle scattering is hosted by the Niels Bohr Institute and the Department of Food Science at the University of Copenhagen. The goal is to provide students with...
by AL
2024.03.04 10:31
Forum: Primary data processing
Topic: Interpretation of Kratky Plot
Replies: 1
Views: 670

Re: Interpretation of Kratky Plot

This paper Franke D, Jeffries CM, Svergun DI. (2018) Machine Learning Methods for X-Ray Scattering Data Analysis from Biomacromolecular Solutions Biophys. J. 114(11), 2485-2492 is basically on dimensionless Kratky plot interpretations. The method is implemented in DATCLASS . But your data are suspic...
by AL
2024.02.13 12:13
Forum: Primary data processing
Topic: How to eliminate artificial osscillations for P(r) plots using datft
Replies: 4
Views: 786

use GNOM

For experimental data please use the indirect Fourier transform program GNOM. If you need to extract the p(r) function from the GNOM *.out file you may run out2pofr gnom.out --output pofr.dat DATFT is a direct Fourier transform program, it may not provide a smooth p(r) on noisy data. For details ple...
by AL
2024.02.13 11:55
Forum: Primary data processing
Topic: error: expected value greater or equal 1 for option 'first', got '-1'".
Replies: 1
Views: 397

please provide more details

Does your file contain three columns (q, I(q), err)? Does your file have the '.dat' extension? Can you attach the file here?
Do you get the error right after you click 'Analysis > Dammif' or at some stage during the manual selection of parameters?
What version of ATSAS are you using?
by AL
2024.01.31 14:08
Forum: Primary data processing
Topic: How to determine the coefficient of determination for Guinier Fits in Primus?
Replies: 2
Views: 606

Re: How to determine the coefficient of determination for Guinier Fits in Primus?

While I can see the fit, I cannot see the coefficient of determination for said fit in this window (i.e. R2). AUTORG and PRIMUS do not calculate the coefficient of determination. Furthermore, there is a difference in the Rg reported in the "Properties" window and the Rg from AutoRg. Why i...
by AL
2024.01.10 13:34
Forum: Model evaluation and manipulation
Topic: Chi2 cutoff
Replies: 4
Views: 1394

Re: Chi2 cutoff

According to this table (slide 19) given the significance level α = 0.01 and the number of points n = 50 the acceptable Chi 2 values are 0.57–1.62. For the significance level α = 0.05 and the number of points n = 50 you can calculate your Chi 2 values in Python: scipy.stats.chi2 .ppf([alpha/2, 1 - a...
by AL
2024.01.09 17:39
Forum: Model evaluation and manipulation
Topic: Chi2 cutoff
Replies: 4
Views: 1394

Re: Chi2 cutoff

Strictly speaking, you need Chi2 ~ 1.0. The exact value depends on the number of data points.
by AL
2024.01.09 17:35
Forum: Mixtures and flexible systems
Topic: EOM for a pentamer with disordered regions
Replies: 3
Views: 1846

Re: EOM for a pentamer with disordered regions

I'm not sure if keeping both structured regions in the same .pdb file will work but you can try.
I'd save them to two separate files and mark them as 'fixed' (instead of 'free').
by AL
2023.12.21 18:09
Forum: Mixtures and flexible systems
Topic: EOM for a pentamer with disordered regions
Replies: 3
Views: 1846

Re: EOM for a pentamer with disordered regions

I am trying to run EOM on a mixture of a protein and a disordered peptide. I don't think you can run EOM online for a mixture of two non-interacting proteins. But you can create two pools of models (one for the pentamer, the other for the peptide) and run FFMAKER on your PC. In EOM online use Advan...
by AL
2023.12.04 09:39
Forum: Ab initio shape determination
Topic: problem running with Dammin in linux
Replies: 6
Views: 1084

dammin --an=P --lm=30

Well, if you have an expected structure (e.g. a protein model from the PDB or AlphaFold ) why don't you fit it to your data with CRYSOL ? If the model doesn't fit - check what is wrong (too small? too extended?..) and try to refine it. If you expect a single rigid model then you can refine your star...
by AL
2023.12.01 14:35
Forum: Ab initio shape determination
Topic: problem running with Dammin in linux
Replies: 6
Views: 1084

dammin --sv ellipsoid

DAMMIN estimates the number of beads ("dummy atoms") for a sphere by default. Then it removes the beads until the model fits the input data. Since the volume of your very elongated model is much smaller than the initial search volume, the number of remaining beads is small. You can try a c...
by AL
2023.11.28 17:10
Forum: Ab initio shape determination
Topic: problem running with Dammin in linux
Replies: 6
Views: 1084

damaver --nbeads

I ran Dammif to obtain my first 10 models in fast mode and average to get different clusters... DAMAVER has an --nbeads option which sets the number of beads within the resulting DA models (including *-damstart.cif I guess). Try increasing that value. I personally wouldn't go through all these step...
by AL
2023.10.05 09:24
Forum: Mixtures and flexible systems
Topic: EOM selected ensembles have a smaller Dmax than measured with GNOM
Replies: 3
Views: 1454

GLYCOSYLATION works with CA-only models

Yes, GLYCOSYLATION should work with RANCH models.
by AL
2023.09.25 17:23
Forum: Mixtures and flexible systems
Topic: EOM selected ensembles have a smaller Dmax than measured with GNOM
Replies: 3
Views: 1454

Use the GLYCOSYLATION tool to add glycans

Yes, glycosylation could be responsible for this difference. Try the GLYCOSYLATION command-line program. You just provide the pdb file of your rigid domain, the number of glycans to be added to that domain and the total molecular weight of the glycan groups to be added. GLYCOSYLATION will add glycan...