Search found 607 matches

by AL
2018.08.15 13:56
Forum: Working with Models
Topic: Criteria for selecting models from Crysol output
Replies: 2
Views: 14

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: 27

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: 70

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: 132

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: 49

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: 70

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: 1
Views: 66

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: 160

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: 132

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: 87

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...
by AL
2018.06.19 10:54
Forum: Feedback
Topic: Education / Outreach sub
Replies: 5
Views: 160

Re: Education / Outreach sub

Dear Peter C, feel free to ask your questions in this thread; we may create a subforum if there will be enough interest.
by AL
2018.06.18 11:21
Forum: Primary Data Processing
Topic: How can I decide Dmax correctly?
Replies: 5
Views: 395

Validate your MW, try DARA, DATCLASS

Fig. 3 looks like your D max is about 265 A. Indeed your s min = 0.013 A -1 , so formally you cannot correctly estimate D max > 242 A. If D max = 265 A fits your expectations (for the MW computed from the sequence) make sure 'Rmax=0' is checked, save and give DAMMIN/DAMMIF a try. Before starting any...
by AL
2018.05.28 11:16
Forum: ATSAS Package in General
Topic: ATSAS release 2.8 is available
Replies: 4
Views: 2353

ATSAS release 2.8.4 is available

Download ATSAS 2.8.4 (academic users only) New platforms (beta): Debian 9 and Ubuntu 18.04. This is the last release for Debian 7. Due to incompatibilities of Qt4 with recent versions of MacOSX, there are no GUI programs (primus, chromixs etc.) in the MacOSX package of ATSAS 2.8.4. Changes in ATSAS...
by AL
2018.05.07 10:14
Forum: ATSAS Package in General
Topic: Removing yellow colour from file names and plot?
Replies: 2
Views: 202

primusqt Line Style

Top right corner, right above the file names there is a drop-down menu "Data" - change it to "Line Style" - you'll be able to change the colour and line width of each data set.
by AL
2018.05.02 16:12
Forum: Ab Initio Shape Determination
Topic: Heterodimer 3D structure fitting on ab initio model
Replies: 1
Views: 188

supcomb

Try:

Code: Select all

supcomb template.pdb dammif.pdb --enantiomorphs=Y
SUPCOMB manual
SUPALM manual