Search found 28 matches

by rambor
2019.12.25 01:03
Forum: SAXS & SANS Software
Topic: SCATTER program file format
Replies: 1
Views: 2599

Re: SCATTER program file format

Hi Han Yin,

I don't regularly read this site, but having looked at your data, the Anton Paar file is nonsense, you have repeated q-values (first column), on top of zeros for error estimates, Scatter rejects it.

Best,

Rob
by rambor
2014.07.01 22:46
Forum: SAXS & SANS Software
Topic: New web server for SAXS/WAXS calculations
Replies: 7
Views: 10590

Re: New web server for SAXS/WAXS calculations

Thanks Jochen,


The results were very nice. Have you seen Peter Moore's recent paper in Biophysical journal regarding corrections to WAXS data?

CRYSOL 1, FOXS 1, WAXSiS 1
by rambor
2014.07.01 12:20
Forum: SAXS & SANS Software
Topic: New web server for SAXS/WAXS calculations
Replies: 7
Views: 10590

Re: New web server for SAXS/WAXS calculations

I tried and it failed after two hours (using single chain from P4-P6 RNA domain crystal structure). 2 hours is quite long to notify someone it didn't work

So far: CRYSOL 1, FOXS 1, WAXSiS 0
by rambor
2014.06.28 00:39
Forum: SAXS & SANS Software
Topic: Pair distribution function
Replies: 2
Views: 9599

Re: Pair distribution function

Kratky plots should be made dimensionless. See Javier Perez's paper from SOLEIL, basically divide I(q) by I(0) and multiply by (q*Rg)^2 with x-axis as q*Rg. For P(r), typically divide by integrated area of the P(r) distribution, this scales to concentration and volume. This can be done with a single...
by rambor
2014.06.28 00:33
Forum: SAXS & SANS Software
Topic: Chi square Free
Replies: 2
Views: 8220

Re: Chi square Free

Its in the latest version of Scatter. Source code is in the jar file under chi-free class
by rambor
2014.06.28 00:10
Forum: SAXS & SANS Software
Topic: SCATTER
Replies: 3
Views: 9733

Re: SCATTER

If this is the Scatter I wrote at SIBYLS, you need JRE 1.7 or greater and the latest version 2.1c at https://bl1231.als.lbl.gov/scatter/ 2.1c can now use some ATSAS tools (DAMMIN/F and datgnom) but you will need to download ATSAS from EMBL and tell scatter where to find the bin directory in "Setting...
by rambor
2012.05.17 20:30
Forum: Rigid Body Modelling
Topic: rigid body modeling with prior bead models and PDB
Replies: 2
Views: 2706

rigid body modeling with prior bead models and PDB

I have SAXS data of a complex where one component is an atomistic PDB model and the other is a bead model from GASBOR. Can SASREF perform rigid body search/refinement using the two models?
by rambor
2011.11.14 12:34
Forum: Working with Models
Topic: CRYSOL and Spherical Harmonics
Replies: 1
Views: 3206

CRYSOL and Spherical Harmonics

Does anyone know if the spherical harmonic expansion uses only the real parts or does it include the imaginary part?

I can't seem to resolve this from the paper as well as the original 1970 paper by Stuhrmann.

Thanks,

Rob
by rambor
2011.09.08 03:08
Forum: Working with Models
Topic: CRYSON batch mode problems
Replies: 11
Views: 7441

resolution on the matter

Has the cryson problem been fixed? I am having the same issue with cryson terminating at around 0.1 A<sup>-1</sup> and not adding more than 51 points.

Thanks
by rambor
2011.06.05 21:45
Forum: Rigid Body Modelling
Topic: SASREF and DAMMIN-damfilt models
Replies: 1
Views: 2497

SASREF and DAMMIN-damfilt models

Can SASREF take as input models DAMMIN/F models that were averaged using damfilt?

I have two proteins that don't change when complexed. I got great data on each of them and the complex so it seems I could use SASREF as a pseudo docking algorithm.
by rambor
2011.06.05 21:42
Forum: Ab Initio Shape Determination
Topic: MONSA compilation error
Replies: 21
Views: 12084

I got everything working. I was using a MONSA file from the webserver and I guess there are some differences, not quite fully compatible. One important thing is to make sure the input data file doesn't contain columns other than q, I(q) and error and that the number of datapoints exactly matches wha...
by rambor
2011.05.30 20:53
Forum: Ab Initio Shape Determination
Topic: MONSA compilation error
Replies: 21
Views: 12084

contents

Yeah, its the latest release, if you look at the error, its looking for something or referencing franke which I imagine is someone in the ATSAS group

Master file for Complex
109 -1.0 0.0 0.0
36.5 -1.0 0.0 0.0
1 1 0.0 0.0
'p65merge.con' -1
'num2_3merge.con' -1
by rambor
2011.05.28 10:27
Forum: Ab Initio Shape Determination
Topic: MONSA compilation error
Replies: 21
Views: 12084

MONSA compilation error

I think there might be a compiling error in MONSA. I am trying to run it on either a MAC or Windows computer and get the same error with the latest release of ATSAS. Log file name .......................... <log>: run1 Project identificator .................................. : run1 Project descripti...
by rambor
2010.07.09 02:19
Forum: Working with Models
Topic: Settling the debate Chi vs Chi-square
Replies: 10
Views: 13253

Settling the debate Chi vs Chi-square

So, we are trying to determine if the Chi value reported by CRYSOL is chi-square or the square root of chi-square? I am betting the value is the square root. Also, the chi-square appears non-standard in that the number of points is not adjusted for by the reduction in degress of freedom required in ...
by rambor
2010.04.19 22:45
Forum: Working with Models
Topic: CRYSOL and shell Rg
Replies: 5
Views: 4261

Just to be clear, the shell Rg is the Rg calculated in the absence of the actual molecule and constitutes only the solvent shell. Is that correct?

Oh, the pdb files they used were 3D0U and 2GIS.

RPR