Search found 28 matches

by emded
2016.10.27 12:22
Forum: Rigid Body Modelling
Topic: Sasref/Coral restraints side-chain atoms and not CA atoms
Replies: 0
Views: 4551

Sasref/Coral restraints side-chain atoms and not CA atoms

Hi,

is it somehow possible to make restraints on specific atoms in the side-chains rather than the CA/backbone atoms?

Emil
by emded
2016.08.30 00:20
Forum: Ab Initio Shape Determination
Topic: MONSA input parameters
Replies: 0
Views: 4757

MONSA input parameters

For the online MONSA version, if i have deuterated and protonated protein, how do i distinguish them? there is the parameters D2fraction and perd1, what are these exactly? and what numbers should be put in if the protein is completely deuterated, 100, or 1.0?

Best,
Emil
by emded
2015.09.29 01:08
Forum: Ab Initio Shape Determination
Topic: DAMMIF ab initio shape of SANS data
Replies: 1
Views: 6442

DAMMIF ab initio shape of SANS data

Hi, is it possible to submit SANS data to DAMMIF analysis, at say 0% D20 or 100% D20 levels, given that I have an RNA-protein complex? Also, is it possible to obtain the shape of the RNA alone at the matchpoint of the protein using DAMMIF? I wonder if it is specific to X-ray scattering and not neutr...
by emded
2015.09.17 12:25
Forum: SAS Experiment Design
Topic: SANS of RNA-Protein Complex
Replies: 9
Views: 12465

Re: SANS of RNA-Protein Complex

Hi again, now we have been able to find the matchpoints experimentally. I wonder how much one needs to determine the curves that are between the matchpoints and how much information that are in these? So lets say we determine the curve at ratio of 0, around 40 (protein), around 70 (rna) and 100. Do ...
by emded
2015.09.09 15:28
Forum: ATSAS Package in General
Topic: PRIMUS on Windows
Replies: 2
Views: 5162

Re: PRIMUS on Windows

Thanks a lot, it works!
by emded
2015.09.09 11:13
Forum: ATSAS Package in General
Topic: PRIMUS on Windows
Replies: 2
Views: 5162

PRIMUS on Windows

Hi, When I run the latest version of Primus on Mac it is much better and seems as the latest than the one running on Windows. I remember from the SAXS course there was a way to get this newest version on Windows as wel, but only running it through the terminal. What was the script for that? In the l...
by emded
2015.09.01 12:13
Forum: SAS Experiment Design
Topic: SANS of RNA-Protein Complex
Replies: 9
Views: 12465

Re: SANS of RNA-Protein Complex

Thanks so much. It works well, however, what i dont understand now is how one can determine the exact matchpoint. Would i need to perform guesses at the deuteration of the solvent to hit matchpoint (try many values randomly) , or is there a function that takes the pdb file and tells the exact deuter...
by emded
2015.08.31 15:55
Forum: SAS Experiment Design
Topic: SANS of RNA-Protein Complex
Replies: 9
Views: 12465

Re: SANS of RNA-Protein Complex

Thanks for the reply. How to use CRYSON to determine the scattering of 1H/2H? Is it possible to run it without an experimental curve and determine the theoretical matchpoint ratio of H20/2H20? I am familiar with CRYSOL but there one needs to add I guess both the experimental curve (.dat) as well as ...
by emded
2015.08.19 14:19
Forum: SAS Experiment Design
Topic: SANS of RNA-Protein Complex
Replies: 9
Views: 12465

Re: SANS of RNA-Protein Complex

Thanks! how is this done in Cryson, perhaps by changing the PDB text file
at those postions where i want to introduce 13C instead of 12C somehow?
by emded
2015.08.03 16:51
Forum: SAS Experiment Design
Topic: SANS of RNA-Protein Complex
Replies: 9
Views: 12465

Re: SANS of RNA-Protein Complex

To be more specific, RNA can be labeled 15C or/and 13C, would they give enough difference
in scattering as to hide/reveal these parts compared to normal unlabeled RNA?
by emded
2015.07.21 12:39
Forum: SAS Experiment Design
Topic: SANS of RNA-Protein Complex
Replies: 9
Views: 12465

SANS of RNA-Protein Complex

Hi
Is it possible to reveal different parts of the RNA molecule in a protein-RNA complex?
For example, to label different parts of it in some way and then use contrast
variation to hide that part of RNA and see all the others?

Kind regards
by emded
2015.01.29 13:35
Forum: Working with Models
Topic: EM to SAXS
Replies: 12
Views: 4967

Re: EM to SAXS

I guess that DAMMIF and DAMMIN must have this function/algorithm as they use bead models to fit to the data, so the information within these programs must be the one to use in this case. You think it is possible to submit the EM model to DAMMIF or DAMMIN and than run a modified run where DAMMIF/DAMM...
by emded
2015.01.29 13:24
Forum: Working with Models
Topic: EM to SAXS
Replies: 12
Views: 4967

Re: EM to SAXS

I wonder if there is a program that can take the bead model and fit it to data? This would be exactly needed in this case. I could send you the files if you want to take a look at them. When I perform Crysol, the scattering from the bead model of EM (generated by EM2DAM) and the scattering from the ...
by emded
2015.01.24 22:14
Forum: Working with Models
Topic: EM to SAXS
Replies: 12
Views: 4967

Re: EM to SAXS

To add more information to that, the scattering curve computed from the bead model does not look like a valid SAXS curve, it is flat all the way to s=0.02 for example. On other hand I get at least something that looks like a SAXS curve when running Crysol (at least in the low s region), at high s re...
by emded
2015.01.24 22:01
Forum: Working with Models
Topic: EM to SAXS
Replies: 12
Views: 4967

Re: EM to SAXS

Hi Alex, i managed to run it in the fitting mode, from the interactive mode (typing em2dam initially). Unfortunetely I do not get a good fit, in fact it is way off. I guess it shouldnt be, since the ab anitio models I obtain with the experimental data are close and similar to the surface envelope of...