Search found 11 matches

by anlarsen
2019.02.27 17:00
Forum: Primary Data Processing
Topic: How to generate the theoretical P(r) curve from pdb files?
Replies: 3
Views: 4500

Re: How to generate the theoretical P(r) curve from pdb files?

OBS
CaPP is now updated with several bug-fixes, and possibility for deuteration (SANS), and possibility for inclusion of explicit H and D. So please use the latest version:

https://github.com/Niels-Bohr-Institute ... ophys/CaPP

- and it's 100% open source
by anlarsen
2019.02.06 18:56
Forum: Working with Models
Topic: resolution effects in Cryson via the fourth column
Replies: 2
Views: 2225

Re: resolution effects in Cryson via the fourth column

Sure I can. Several SANS beamlines provide a fourth column in data, e.g. these: QUAKKA@ANSTO D22@ILL ... and probable many more. The fourth column provides an uncertainty on the estimated q-value (1 sigma, assuming normal distributions). Documented e.g. here: https://www.ncnr.nist.gov/staff/hammouda...
by anlarsen
2019.01.24 10:06
Forum: Working with Models
Topic: resolution effects in Cryson via the fourth column
Replies: 2
Views: 2225

resolution effects in Cryson via the fourth column

Dear ATSAS (cryson) developers, most SANS beamlines nowadays provide the resolution effect via an uncertainty of q, in the fourth column of data. However, as of now it is not possible to use this information to take resolution effects into account in Cryson. I know, that one can provide a resolution...
by anlarsen
2018.08.19 13:20
Forum: Primary Data Processing
Topic: How to generate the theoretical P(r) curve from pdb files?
Replies: 3
Views: 4500

Re: How to generate the theoretical P(r) curve from pdb files?

Dear Zhuwenkai, CaPP can calculate the theoretical p(r) directly from a PDB file (without any detour into reciprocal space): https://github.com/Niels-Bohr-Institute-XNS-StructBiophys/CaPP When comparing p(r) functions, I recommend normalising the maximum value to unity (i.e. divide by max{p(r)}), as...
by anlarsen
2018.02.08 15:40
Forum: Rigid Body Modelling
Topic: Increase number of Harmonics in SASREF CV
Replies: 2
Views: 3486

Re: Increase number of Harmonics in SASREF CV

Ok. Thanks for your reply Al! and thanks for the good suggestions. I might try that. It would be a nice feature though - especially as SANS instruments get better, and we can se more features at high-q. But I understand that you all have many ideas and projects for developing the ATSAS package (and ...
by anlarsen
2018.01.23 01:26
Forum: Rigid Body Modelling
Topic: Increase number of Harmonics in SASREF CV
Replies: 2
Views: 3486

Increase number of Harmonics in SASREF CV

Dear ATSAS developers, I wish to increase the number of harmonics in a SASREF CV refinement. I can see, when modelling in cryson, that it is necessary, due to the size of the protein, to increase the number of harmonics from the default 15, even when the protein is centered. It is a 210 kDa pentamer...
by anlarsen
2018.01.23 01:02
Forum: Rigid Body Modelling
Topic: SASREFMX Help
Replies: 1
Views: 7428

Re: SASREFMX Help

The manual for SASREF MX: https://www.embl-hamburg.de/biosaxs/manuals/sasrefcvmx.html I can recommend running SASREF online , where you have the option to run SASREF MX, then the online version will generate the needed files, which you can use as templates for running it in offline batch mode. Best ...
by anlarsen
2017.05.30 08:04
Forum: Working with Models
Topic: Atomic form factors and incoherent scattering in Cryson
Replies: 1
Views: 3161

Atomic form factors and incoherent scattering in Cryson

Dear ATSAS team, In Cryson, do you use an atomic form factors for the nuclei, or simply use that the form factor is effectively unity (i.e. that nuclei can be considered as points)? The second option, I suppose? In prediction mode, do you include the incoherent scattering (mainly from H in the sampl...
by anlarsen
2017.05.30 07:46
Forum: Working with Models
Topic: Volumes used by crysol
Replies: 5
Views: 4652

Re: Volumes used by crysol

Dear ATSAS team, You write "Displaced volume is the sum of the Van-der-Waals volumes of individual atomic groups, (i.e. it serves as V0 in formula)" But the Crysol article (1995) lists volumes from (1) Fraser et al. (1978) and from International Tables of X-ray Crystallography (1968). Are these volu...
by anlarsen
2017.03.16 12:18
Forum: Working with Models
Topic: Ignore deuterium in CRYSON
Replies: 4
Views: 3809

Re: Ignore deuterium in CRYSON

Great, thank you SaxsMax
by anlarsen
2017.03.07 11:08
Forum: Working with Models
Topic: Ignore deuterium in CRYSON
Replies: 4
Views: 3809

Ignore deuterium in CRYSON

Hi,

I am calculating a SANS curve from a PDB structure using CRYSON. The PDB has H's and D's added (with PHENIX). When saying "No" to the option "Account for explicit hydrogens? [ Y / N ]", I ignore the H's. But apparently the D's are not ignored. Shouldn't they be?

/Andreas