Search found 642 matches

by AL
2018.12.24 13:18
Forum: Announcements
Topic: ASEAN workshop AWSAXS2019
Replies: 2
Views: 555

Re: ASEAN workshop AWSAXS2019

akgupta wrote:
2018.12.21 17:34
I just wanted to know what are the topics will be covered in this workshop? WIll you cover theory part as well?
Sure, a bit of theory, a bit of practice, a quite broad range of topics will be covered. Please check the AWSAXS2019 Program for details.
by AL
2018.12.21 16:52
Forum: Announcements
Topic: ASEAN workshop AWSAXS2019
Replies: 2
Views: 555

ASEAN workshop AWSAXS2019

https://www.embl-hamburg.de/biosaxs/img/awsaxs2019.png ASEAN Workshop on Small Angle X-ray Scattering 19 - 26 February 2019 SLRI, Thailand The ASEAN Workshop on SAXS targets scientists, researchers, lecturers, postdocs and PhD students who are interested in determination of protein structure in sol...
by AL
2018.12.21 13:20
Forum: Primary Data Processing
Topic: Different Rg
Replies: 1
Views: 346

Rg in CRYSOL output

2) Final Radius of gyration calculated from pdb file, after fitting to the experimental curve - is this "Theoretical Rg" or "Rg" in crysol_summary.txt Yes, this value is called: "Rg from the slope of net intensity" in the log file; in 'crysol_summary.txt' it is called "Theoretical Rg" if CRYSOL was...
by AL
2018.11.29 12:45
Forum: Primary Data Processing
Topic: Molecular weight estimation
Replies: 4
Views: 520

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: 1177

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: 1807

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: 1923

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: 978

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: 1433

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: 1471

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: 2119

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: 4255

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: 1121

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: 978

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: 989

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...