Search found 642 matches

by AL
2018.09.17 13:13
Forum: Primary Data Processing
Topic: Extracting P(r) to Excel?
Replies: 2
Views: 907

incomplete data in gnom.out

Your file appears to be corrupt - the actual data are missing. It comes from an older version of GNOM; make sure you have the latest version of ATSAS installed and reprocess your data following these instructions (steps 1-6).
by AL
2018.08.29 16:39
Forum: ATSAS Package in General
Topic: ATSAS download down to maintenance
Replies: 2
Views: 1245

ATSAS download available

The ATSAS download page is back online.
by AL
2018.08.29 12:24
Forum: ATSAS Package in General
Topic: ATSAS download down to maintenance
Replies: 2
Views: 1245

Re: ATSAS download down to maintenance

Moving to a new FTP server is taking longer than expected. This will be resolved within a few hours. Apologies for the inconvenience.
by AL
2018.08.28 11:44
Forum: Primary Data Processing
Topic: Data extrapolation required?
Replies: 1
Views: 1247

Re: Data extrapolation required?

QUESTION 1: the wild-type and mutant A are fine, different concentrations do not change Rg or Dmax... Mutant_A/S?.dat: from the rather narrow concentration range of 0.6-2.1 mg/ml I'd say there are concentration effects: the Guinier R g increases with concentration from 2.6 to 3.0 nm. The extrapolat...
by AL
2018.08.27 15:19
Forum: Mixtures and Flexible Systems
Topic: EOM online vs local : different results
Replies: 2
Views: 939

EOM online command line options

I ran EOM on my computer with default parameters and it's turned out that they are totally different from those obtained with EOM online. Could you please be more specific? Are you sure you are running the latest version of ATSAS ? EOM online runs with arguments like these: $ eom sequence.seq --qua...
by AL
2018.08.15 13:56
Forum: Working with Models
Topic: Criteria for selecting models from Crysol output
Replies: 2
Views: 1021

Re: Criteria for selecting models from Crysol output

I am working on a two-domain protein. Two domains are connected with a small linker. Structure of one of the domains is solved from one organism and that of other is known from the other organism. You may try CORAL to fit your experimental data with a single model or EOM to fit your data with an en...
by AL
2018.08.09 17:20
Forum: Primary Data Processing
Topic: Merge in Primus
Replies: 1
Views: 861

merge in primusqt

I guess you mean the "old" primusqw on Windows. Please download the latest ATSAS version and open your dat files in the "new" primus qt (on Windows it is called "SAS Data Analysis" in the Start menu). The top file will be used as a reference for the 'Merge' and 'Scale' operations (found under the 'P...
by AL
2018.08.07 17:26
Forum: Ab Initio Shape Determination
Topic: Help with GNOM/Gasbor
Replies: 3
Views: 1177

GNOM parameters

Left plot log(I) vs. s : fit of the Fourier transform of p(r) (blue line) to the experimental SAS data (black dots). The fit is computed like this: I(s) = 4Π ∫ o Dmax p(r) sin(sr)/sr dr Right plot p(r) vs. r : pair distance distribution function. Total quality estimate ranges between 1.0 (best) and...
by AL
2018.08.03 12:51
Forum: Ab Initio Shape Determination
Topic: Chi-square values < 1
Replies: 3
Views: 1245

Re: what can I do to avoid overestimation?

Redo the radial averaging. E.g. if you use pyFAI - switch "pixel splitting" to "No splitting".
by AL
2018.08.03 12:44
Forum: Primary Data Processing
Topic: Guinier parameters
Replies: 1
Views: 913

PRIMUS Guinier wizard parameters

I 0 : Forward scattering I(0). R g : Radius of gyration - the average of square center-of-mass distances in the molecule (weighted by the scattering length density). It is a measure for the overall size of a macromolecule. If the experimental data are in inverse angstroms (Å -1 ), R g is provided i...
by AL
2018.08.03 11:25
Forum: Ab Initio Shape Determination
Topic: Help with GNOM/Gasbor
Replies: 3
Views: 1177

Use PRIMUSqt and GASBOR online

1. Make sure you have the latest ATSAS version installed. 2. Open your background-subtracted data in PRIMUS (on Windows make sure you use primusqt; it is called "SAS Data Analysis" in the Start menu). 3. In the bottom right panel go to the 'Analysis' tab and click Distance Distribution'. This will s...
by AL
2018.07.31 15:36
Forum: Mixtures and Flexible Systems
Topic: GAJOE no PDB output in file / CaCa_dist file doesnt look right
Replies: 4
Views: 1807

limitations of a custom EOM pool

I am running GAJOE on a pool of 10k pdb files I generated with TraDES. ... 1 - It looks like I had to get 17 pdbs in pdbs directory but there is none. I don't think GAJOE can reproduce the ensemble models if the models were not generated by RANCH. 2 - I get a good fit (judged from profiles.fit), re...
by AL
2018.07.24 17:29
Forum: Feedback
Topic: Education / Outreach sub
Replies: 5
Views: 2582

Re: Education / Outreach sub

1. what broad categories of problems/phenomena are solved/investigated with SAX SAX S stands for Small Angle X-ray S cattering. This technique can be applied to a wide range of problems. On this Forum we primarily discuss scattering of macromolecules in solution - typically SAXS studies of proteins...
by AL
2018.07.23 16:08
Forum: Ab Initio Shape Determination
Topic: Chi-square values < 1
Replies: 3
Views: 1245

Re: Chi-square values < 1

BC_Flügge wrote:
2018.06.15 10:16
I try to build ab initio models with DAMMIF/GASBOR and I am always getting Chi-squares values < 1 (usually, around 0.4 - 0.6) no matter what.
The experimental errors (3rd column in your HtrASn.dat file) are clearly overestimated - that's why the chi-squared values are too low.
by AL
2018.07.23 16:02
Forum: Ab Initio Shape Determination
Topic: Primus qt Dammif
Replies: 2
Views: 952

dammif Output Files

*-1.pdb - represents the modelled particle. Open it with with PyMOL. *.fir - fit of the simulated scattering curve versus the experimental data. Open it with primus or sasplot. You will find a detailed description in the Output Files section of the DAMMIF manual . Check out the EMBO practical course...