Search found 624 matches

by AL
2018.11.29 12:45
Forum: Primary Data Processing
Topic: Molecular weight estimation
Replies: 2
Views: 54

Re: Molecular weight estimation

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...
by AL
2018.11.14 19:06
Forum: Mixtures and Flexible Systems
Topic: EOM on disordered peptides
Replies: 1
Views: 883

use I(q) vs. q data files

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.
by AL
2018.11.14 18:54
Forum: Mixtures and Flexible Systems
Topic: GAJOE no PDB output in file / CaCa_dist file doesnt look right
Replies: 4
Views: 1230

Re: limitations of a custom EOM pool

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 ...
by AL
2018.11.14 18:31
Forum: Working with Models
Topic: How to trim SAXS data that it won't come useless
Replies: 1
Views: 1506

where does the 256 points limitation come from?

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 ...
by AL
2018.11.14 17:58
Forum: Mixtures and Flexible Systems
Topic: EOM - software issues
Replies: 3
Views: 610

Re: EOM - software issues

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.
by AL
2018.11.08 12:17
Forum: Rigid Body Modelling
Topic: Assembly a multi-domain protein from available mono-domain?
Replies: 5
Views: 871

try SASREF online

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...
by AL
2018.11.08 11:54
Forum: Primary Data Processing
Topic: How to reduce data points correctly in SAXS scattering data?
Replies: 1
Views: 1142

datregrid

Try datregrid. E.g.

Code: Select all

datregrid --join 3 file.dat
will join every 3 points by averaging.

To reduce the data q range use datcrop.
by AL
2018.11.08 11:49
Forum: ATSAS Package in General
Topic: ATSAS 2.8.4 for MacOSX
Replies: 1
Views: 1324

no GUI programs in the MacOSX 2.8.4 package

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.
by AL
2018.10.13 16:00
Forum: ATSAS Package in General
Topic: ATSAS release 2.8 is available
Replies: 6
Views: 3331

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: 734

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: 3
Views: 610

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: 609

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: 569

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: 965

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: 965

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.