Search found 616 matches

by AL
2018.10.13 16:00
Forum: ATSAS Package in General
Topic: ATSAS release 2.8 is available
Replies: 6
Views: 2608

Re: ATSAS release 2.8 is available

I've downloaded ATSAS 2.8.4, installed it for a Mac (OS 10.13.6) but can't seem to find primus in the package. My ATSAS is currently stored in the 'Applications' folder. Am I missing something? Yes, you are: Due to incompatibilities of Qt4 with recent versions of MacOSX, there are no GUI programs (...
by AL
2018.09.28 14:44
Forum: Mixtures and Flexible Systems
Topic: Error : Gajoe : Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Replies: 1
Views: 96

Install latest ATSAS

vas2201 wrote:
2018.09.21 22:05
******* GAJOE - version 2.1 - (r7883) *******
This is a bit outdated. Please download the latest ATSAS version and follow these instructions.
by AL
2018.09.28 14:35
Forum: Mixtures and Flexible Systems
Topic: EOM - software issues
Replies: 2
Views: 59

EOM/ATSAS version?

Are you using EOM online or on your PC? Is there an error message?
by AL
2018.09.17 13:29
Forum: Mixtures and Flexible Systems
Topic: EOM ensemble has poor fit to scattering at high q
Replies: 2
Views: 82

gajoe --no-constant

The fit is okay at low q... It's not okay - the Guinier region is not fitted: the R g of your experimental data is clearly greater than R g of your fit. Does the molecular weight estimated from your experimental data match the molecular weight calculated from your protein sequence? ... but at highe...
by AL
2018.09.17 13:13
Forum: Primary Data Processing
Topic: Extracting P(r) to Excel?
Replies: 2
Views: 72

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: 486

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: 486

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: 538

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: 128

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: 168

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: 156

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: 227

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: 290

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: 169

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: 227

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...