Search found 642 matches

by AL
2018.03.05 14:19
Forum: Announcements
Topic: EMBO practical course on solution scattering 2018
Replies: 0
Views: 2784

EMBO practical course on solution scattering 2018

https://www.embl-hamburg.de/biosaxs/courses/embo2018/img/embo-2018-hamburg.jpg EMBO practical course on solution scattering from biological macromolecules 19 - 26 November 2018 EMBL Hamburg The Course is aimed at young scientists working in the field of structural biology: biochemists, biophysicist...
by AL
2018.02.22 16:28
Forum: Mixtures and Flexible Systems
Topic: EOM on a homo-oligiomer
Replies: 8
Views: 1860

Re: EOM on a homo-oligiomer

Then try providing the domain with the oligomerization interface as a heptamer and the other domain as a monomer:
  • Overall symmetry: P7
    Sequence: [monomeric sequence]
    Number of domains: 2
    Domain 1: [multimer][fixed]
    Domain 2: [monomer][fixed]
by AL
2018.02.21 14:42
Forum: Mixtures and Flexible Systems
Topic: EOM on a homo-oligiomer
Replies: 8
Views: 1860

Re: EOM on a homo-oligiomer

Align your heptamer with ALPRAXIN . Open the aligned pdb file in a text editor, leave one monomer (any), remove the other six. Further split this monomer into two domains which should be connected by the internal flexible loop. Run EOM online : Overall symmetry: P7 Sequence: [monomeric sequence] Num...
by AL
2018.02.05 14:28
Forum: Rigid Body Modelling
Topic: Increase number of Harmonics in SASREF CV
Replies: 2
Views: 1959

Re: number of Harmonics in SASREF CV

Increasing the number of harmonics in SASREF is technically challenging. It is not planned to release a version of SASREF/CV/MX with more than 15 harmonics in the nearest future. You may try to shorten the fitting range to see if this improves the modelling. Use constant subtraction. You may do mult...
by AL
2017.12.13 13:33
Forum: Mixtures and Flexible Systems
Topic: Which program to use to model protein modified by DNA?
Replies: 2
Views: 1360

Re: Which program to use to model protein modified by DNA?

(It's not clear if your protein is partially unfolded. I'll assume it is well folded.) If you have a model of the protein - start with comparing fitting it to your "unmodified protein" SAXS data with CRYSOL . You may try to improve the fit with SREFLEX . If you have a model of the DNA you may model...
by AL
2017.12.07 14:17
Forum: Mixtures and Flexible Systems
Topic: EOM to model flexible C-terminus on dimeric protein
Replies: 1
Views: 1095

Re: EOM to model flexible C-terminus on dimeric protein

Number of residues per chain: 254 Alignment Problems: check the sequence and the domains Please run pdb2seq on your crystal structure - this will give you the sequence. Note that in case of a dimer you will get the same sequence twice. Please compare it in a text editor to the sequence provided to ...
by AL
2017.12.07 14:03
Forum: Mixtures and Flexible Systems
Topic: Sreflex DNS
Replies: 2
Views: 1148

ATSAS 2.8.3 is out

sasha wrote:This is fixed in ATSAS 2.8.3
Version 2.8.3 is out, please update your ATSAS.
by AL
2017.12.06 11:23
Forum: ATSAS Package in General
Topic: ATSAS release 2.8 is available
Replies: 6
Views: 4255

ATSAS release 2.8.3 is available

Download ATSAS 2.8.3 (academic users only) This is the last release for the following platforms: Ubuntu 12; openSUSE 13. Changes in ATSAS 2.8.3: New program datmw: unified access to multiple estimates of molecular weight; chromixs : added entry to Start and applications folders for each platform, a...
by AL
2017.12.05 16:49
Forum: Ab Initio Shape Determination
Topic: DAMMIN data input not matching GNOM
Replies: 1
Views: 1215

GNOM JOB = 4

It looks like you've used GNOM to calculate the distance distribution function of the cross-section for a monodisperse system of rod-like particles (JOBTYP = 4). DAMMIN assumes it is a distance distribution function of the whole particle - I don't think it can build a model based on the cross-sectio...
by AL
2017.11.06 12:38
Forum: Mixtures and Flexible Systems
Topic: EOM as a dimer with no PDBs
Replies: 2
Views: 1221

use a very short dimer

If you know the dimerization interface you may use a very short dimer that consists of just a few residues.
You may also want to try EOM without symmetry (just provide the same sequence twice).
by AL
2017.11.06 11:46
Forum: Mixtures and Flexible Systems
Topic: EOM fits to a slightly different data profile
Replies: 4
Views: 1960

log plot vs. linear plot

...if the substracted background is constant then why the original data are superimposed within the low resolution region and then mismatch in the upper resolution region. Because you are looking at it on a logarithmic scale. Plot it on a linear scale and it will be obvious that it is just a consta...
by AL
2017.11.02 12:41
Forum: Mixtures and Flexible Systems
Topic: EOM fits to a slightly different data profile
Replies: 4
Views: 1960

Constant subtraction

EOM (well, actually CRYSOL) subtracts a small constant to compensate imperfect background subtraction. In your case the constant was negative.
Make sure next time you remove the very low angles that don't follow the Guinier law from your data.
by AL
2017.10.05 11:35
Forum: Working with Models
Topic: Deriving chi2 from two SAXS curves
Replies: 2
Views: 1612

OLIGOMER

OLIGOMER is what you are looking for.
You have to prepare the form-factors file with the program FFMAKER or in a text editor before running OLIGOMER.
by AL
2017.10.02 15:27
Forum: Mixtures and Flexible Systems
Topic: EOM - Using two models with internal P2 symmetry
Replies: 12
Views: 3726

Re: "sub-select" a better frame range

I suspect the "not super goodness" might be due to the fact that the frames I used are not 100% monodisperse (...) Any ideas on how I could maybe "sub-select" a better frame range? You can open your frames in CHROMIXS and try to manually select only one side of the peak. Of course it would be bette...