Search found 8 matches

by dggreene
2015.11.24 23:52
Forum: Ab Initio Shape Determination
Topic: smearing for neutron scattering/access to source code
Replies: 0
Views: 6340

smearing for neutron scattering/access to source code

I am interested in using MONSA to perform ab initio shape determination from a PEGylated protein molecule. However, my data are smeared and MONSA (or ATSAS in general) requires a resolution file. I do not have this resolution file, but I do have dQ information which can be used for Gaussian smearing...
by dggreene
2015.04.07 16:09
Forum: Working with Models
Topic: Change solvent density in CRYSON batch mode
Replies: 0
Views: 4565

Change solvent density in CRYSON batch mode

Hi I am wondering if there is an option to change the solvent scattering density in CRYSON batch mode. I see there are options to change the D2O content and the density of the hydration shell but as far as I can see there is no option to change the solvent density. Unfortunately my sld lies outside ...
by dggreene
2014.01.06 18:30
Forum: Working with Models
Topic: Excluded volume fit in CRYSOL
Replies: 5
Views: 4286

Re: Excluded volume fit in CRYSOL

Does eqn 1 from the paper then become,
I(s) = <|Aa(s)+ (V/V0)*p0*Ac(s)+dp*Ab(s)|^2>omega ?

Also, is V0 part of the output log file?

Thanks
by dggreene
2014.01.06 16:47
Forum: Working with Models
Topic: Excluded volume fit in CRYSOL
Replies: 5
Views: 4286

Re: Excluded volume fit in CRYSOL

Ok.

How does the excluded volume enter into the calculation now that it is decoupled?

Do you have more up to date documentation about the specifics of the calculation?

Thanks
by dggreene
2013.12.18 21:43
Forum: Working with Models
Topic: Excluded volume fit in CRYSOL
Replies: 5
Views: 4286

Excluded volume fit in CRYSOL

Hi In the CRYSOL paper it lists only 2 adjustable parameters in the fit, the density of the hydration layer and the effective atomic radius, r0. However, there are 3 adjustable parameters in the software, the density of the hydration layer, the optimal atomic radius,Ra, and the excluded volume. The ...
by dggreene
2013.04.11 01:16
Forum: Working with Models
Topic: Scaling intensities from CRYSON
Replies: 1
Views: 6692

Scaling intensities from CRYSON

I am trying to put the calculated intensity on the same scale as my data. From my understanding, the calculated intensity has units of cm^2 and it is the scattering cross-sectional area for one molecule, taking the solvent and hydration layer into account. To convert to absolute intensity (1/cm) I m...
by dggreene
2013.04.03 21:00
Forum: Working with Models
Topic: Max number of atoms in CRYSON
Replies: 2
Views: 2565

Re: Max number of atoms in CRYSON

Thanks for the quick reply! I sent you the information you requested.

I am going to try to recompile the software. Where can I find the source code?
by dggreene
2013.04.03 19:29
Forum: Working with Models
Topic: Max number of atoms in CRYSON
Replies: 2
Views: 2565

Max number of atoms in CRYSON

I am trying to calculate the scattering from a large protein complex (about 75 protein molecules ~2e5 atoms). When I load the pdb file, CRYSON crashes without giving an error (at least none listed in the log). Is there a maximum number of atoms CRYSON can calculate? If so, is there any way to increa...