SAXS

I just started to used the new version of Primus (from 2.8.3 package)... If your OS is Windows or Linux - please note that the latest package is 2.8.4. (If you have a Mac please stick to 2.8.3 for now.) I was wondering if there was any help/manual with further details about the different results, s...

You should use I(q) vs. q background-subtracted experimental data files (*.dat) in ASCII format containing 3 columns: (1) momentum transfer q, (2) experimental intensity I(q) and (3) experimental errors.
Before interpreting the Rg histograms make sure the fit to your data is good.

How are the intensity profiles from given own pool of pdbs are created if the pool is not generated by RANCH? If you used your own pool of models then RANCh was not involved. The intensities are calculated by CRYSOL if you run GAJOE with the --pool option . Also in the log file, the pdb models are ...

I am using one program that can only process SAXS data containing 256 or less data points. ... ENSEMBLE contain three external programs and one of them is CRYSOL. I guess your question about rebinning data is already answered . But where does the 256 points limitation come from? CRYSOL can compute ...

nb_1993 wrote: ↑

2018.10.04 14:44

I was using EOM on my PC. There weren't any error messages , its just closed .

What ATSAS version? Any error messages in the log?
Please run it online and send us the job id so we can investigate it.

Try SASREF online . Step 1 Experimental data: SAXS (X-ray) only, standard Number of curves: 1 Number of subunits: 2 Overall symmetry: P1 Step 2 Provide your experimental SAXS data and the two subunits. Check 'Provide contact conditions'. Step 3 Provide one contact condition by choosing the last resi...

Try datregrid. E.g. will join every 3 points by averaging.

To reduce the data q range use datcrop.

According to the ATSAS download page, due to incompatibilities of Qt4 there are no GUI programs (primus, chromixs etc.) in the MacOSX package of ATSAS 2.8.4, please use 2.8.3 for MacOSX instead.

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 (...

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This is a bit outdated.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.

Are you using EOM online or on your PC? Is there an error message?

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...

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).

The ATSAS download page is back online.

Moving to a new FTP server is taking longer than expected. This will be resolved within a few hours. Apologies for the inconvenience.