Search found 696 matches

by Alex
2017.03.26 17:50
Forum: SAXS & SANS Software
Topic: datasw - tool to analyse HPLC-SAXS data
Replies: 2
Views: 11492

Re: datasw - tool to analyse HPLC-SAXS data

Dear All,

Update of DATASW is now available:
https://sourceforge.net/projects/datasw ... tasw-v1.2/

Changes since DATASW v1.1 include following:
* compatible with latest ATSAS 2.8.0
* a number of fixes and improvements
* DATASW now depends on GNUPLOT/QT

Thank you for using DATASW!
Alex
by Alex
2017.03.22 11:00
Forum: Primary Data Processing
Topic: datclass: parse error (only on Ubuntu 14.04)
Replies: 2
Views: 5938

Re: datclass: parse error (only on Ubuntu 14.04)

Hi Daniel
yeah, you are right - i started with installation using *tar.gz and had ATSAS variables
set in my bashrc, whereas then i switched to synaptic manager installation without reverting changes
in my bashrc.

thanks, Alex
by Alex
2017.03.21 22:45
Forum: Primary Data Processing
Topic: datclass: parse error (only on Ubuntu 14.04)
Replies: 2
Views: 5938

datclass: parse error (only on Ubuntu 14.04)

I installed ATSAS 2.8.0 using synaptic package manager on ubuntu 14.04. when using 'datclass' i get the following error: $ /usr/bin/datclass --rg=2.96 --i0=88.2 bsa_00583.out : parse error $ /usr/bin/datclass --rg=2.96 --i0=88.2 bsa_00583.dat : parse error and ..:) /usr/bin/datclass : parse error Ot...
by Alex
2017.03.13 16:25
Forum: Primary Data Processing
Topic: How can I determine the data's Dmax with the ATSAS(2.8)?
Replies: 2
Views: 5728

Re: How can I determine the data's Dmax with the ATSAS(2.8)?

How can I determine the data's Dmax accurately with the ATSAS(2.8)? In which gnom has no interactive mode to view the p(r) function variation while I changing the value of Dmax. Is not there an interactive mode for determining Dmax in Primus? Is the Dmax value important for the beads model building...
by Alex
2017.03.08 14:50
Forum: Working with Models
Topic: CRYSOL:deal with the missing part in the pdb file?
Replies: 2
Views: 5699

Re: CRYSOL:deal with the missing part in the pdb file?

and how can i add the missing part to the structural model to make it complete?
use BUNCH and/or CORAL.
by Alex
2017.03.07 13:49
Forum: Primary Data Processing
Topic: atsas-2.8.0: datgnoms and partistr/parcoor?
Replies: 2
Views: 5332

Re: atsas-2.8.0: datgnoms and partistr/parcoor?

Thanks for the reply! If Rg is not provided datgnom4 determines it internally; the way how Rg is determined is not consistent with autorg and not easily reproducible. In certain cases datgnom4 finds a wrong Rg which leads to a wrong Dmax. It is strongly recommended to provide the --rg option to datg...
by Alex
2017.03.06 23:04
Forum: Primary Data Processing
Topic: atsas-2.8.0: datgnoms and partistr/parcoor?
Replies: 2
Views: 5332

atsas-2.8.0: datgnoms and partistr/parcoor?

Dear ATSAS developers, In whatsnew.txt there is a line: Changes ATSAS-2.8.0 =================== Renamed programs ================= * gnom5 - renamed to gnom * datgnom5 - renamed to datgnom Removed programs ================= * datgnom (version 4) -- However, there is still datgnom4 present in the pac...
by Alex
2017.02.23 17:34
Forum: Mixtures and Flexible Systems
Topic: SREFLEX Chi2 and RMSD meaning ?
Replies: 14
Views: 4927

Re: SREFLEX Chi2 and RMSD meaning ?

Sasha, thanks for your replies!
by Alex
2017.02.21 11:49
Forum: Mixtures and Flexible Systems
Topic: SREFLEX Chi2 and RMSD meaning ?
Replies: 14
Views: 4927

Re: SREFLEX Chi2 and RMSD meaning ?

Sasha, just to re-phrase my questions and give a real life example: I have a protein-DNA complex for which there is a SAXS data. In this complex protein is assumed to be in an opened conformation however the protein only could have been crystallized and its in the closed state. If one places DNA in ...
by Alex
2017.02.15 20:44
Forum: Mixtures and Flexible Systems
Topic: SREFLEX Chi2 and RMSD meaning ?
Replies: 14
Views: 4927

Re: SREFLEX Chi2 and RMSD meaning ?

Yes, any distance below 2.5 between centroids (Calpha por proteins, or C1' for nucleotides) is considered a clash. Then a score is computed as the percentage of clashing centroids in the structure divided by 10 (i.e. a clashes score of 1.0 would represent 10 percent of the centroids clashing). That...
by Alex
2017.02.06 22:30
Forum: Mixtures and Flexible Systems
Topic: SREFLEX Chi2 and RMSD meaning ?
Replies: 14
Views: 4927

Re: SREFLEX Chi2 and RMSD meaning ?

can i ask also how the clash score is calculated? can you also tell more how protein-ligand complexes are treated (where ligand is HETATM, like DNA/RNA/sugars) and how (if) clashscore is calculated for them?
Thank you in advance, Sasha!
by Alex
2017.02.06 16:58
Forum: Mixtures and Flexible Systems
Topic: SREFLEX Chi2 and RMSD meaning ?
Replies: 14
Views: 4927

Re: SREFLEX Chi2 and RMSD meaning ?

i would think that the Chi2 is the discrepancy to scattering data, RMSD to initial model and a clash number for nma-refined model.
HTH, Alex
by Alex
2017.02.03 19:08
Forum: Working with Models
Topic: Crysol High chi
Replies: 3
Views: 6127

Re: Crysol High chi

I think your question belongs to a topic "Working with Models", nevertheless, the fit itself does not look bad, but (i) looks like its data from SWING, (ii) looks like its SEC-SAXS, and if (i) and (ii) are correct, it is not quite clear how you got the final curve (homogeneous Rg range, multiple pea...
by Alex
2017.01.16 18:51
Forum: Mixtures and Flexible Systems
Topic: Rg
Replies: 18
Views: 6470

Re: Rg

hi Heather
i can give it a try as I think I have the right tools to do what you need. Let's take this off the forum - send me an email to ... AT gmail . com
Best, Alex
by Alex
2017.01.13 15:27
Forum: Mixtures and Flexible Systems
Topic: Rg
Replies: 18
Views: 6470

Re: Rg

you can probably play with constraints and represent flexible protein as a set of linkers (LINK 99 + LINK 99 ..etc), however, i am not sure if loop database of CORAL would have enough conformational sampling for your particular case. CORAL is not really meant for flexible molecules. I'd say it is me...