Search found 691 matches

by Alex
2017.03.07 13:49
Forum: Primary Data Processing
Topic: atsas-2.8.0: datgnoms and partistr/parcoor?
Replies: 2
Views: 3163

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: 3163

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: 3800

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: 3800

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: 3800

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: 3800

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: 3800

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: 3772

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: 4805

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: 4805

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...
by Alex
2017.01.13 14:56
Forum: Mixtures and Flexible Systems
Topic: Rg
Replies: 18
Views: 4805

Re: Rg

used EOM for the flexible protein, but was unsure about how best to do this for the binary complex. I gave is a try by inserting the sequence of the globular protein directly in the middle of it's predicted binding site in the flexible protein. I don't think that I did this right though, so didn't ...
by Alex
2017.01.13 13:15
Forum: Mixtures and Flexible Systems
Topic: Rg
Replies: 18
Views: 4805

Re: Rg

The predicted Rg for the flexible protein is 45 A assuming that it is a typical IDP (from Flory's equation using R0 and v parameters in Tria et al., 2015). Yet the experimental Rg at 52 A is higher. there can be a concentration effect too. Did you extrapolate the data to infinite dilution? The reas...
by Alex
2017.01.13 12:34
Forum: Mixtures and Flexible Systems
Topic: Rg
Replies: 18
Views: 4805

Re: Rg

I think the real question here is how to differentiate an extended rigid protein from flexible protein using SAXS? I think in general one should have an idea if the protein is rather extended (e.g. has a rod shape). If not, one can check dimensionless Kratky plot with references to well folded and n...
by Alex
2017.01.10 13:05
Forum: Working with Models
Topic: Reliability of Crysol theoretical curves
Replies: 5
Views: 4537

Re: Reliability of Crysol theoretical curves

Perhaps, analysis of SAXS data as done in the following article can help you:
http://www.pnas.org/content/108/16/6409.long

Alex
by Alex
2017.01.10 13:01
Forum: Rigid Body Modelling
Topic: Coral seem to change scattering data in fitting?
Replies: 1
Views: 2965

Re: Coral seem to change scattering data in fitting?

i think it is because constant subtraction results in oversubtracting. In general for CORAL range till 0.25 1/A is enough and then when the modeling is finished you can fit to the full data range with CRYSOL. In you case, you can remove some data points till 0.48 1/A or so, so that the constant valu...