Search found 24 matches

by Nyshae
2017.02.16 13:58
Forum: Mixtures and Flexible Systems
Topic: SREFLEX Chi2 and RMSD meaning ?
Replies: 14
Views: 3956

Re: SREFLEX Chi2 and RMSD meaning ?

Hi all, Thanks again for the answers! Sasha, to answer your questions, I did run DAMMIF using the online version and generated 20 models. All of them but one were deemed good enough to be superimposed, with a mean value of NSD of 0,597. I also just run ambimeter as you suggested and the output is th...
by Nyshae
2017.02.07 12:56
Forum: Mixtures and Flexible Systems
Topic: SREFLEX Chi2 and RMSD meaning ?
Replies: 14
Views: 3956

Re: SREFLEX Chi2 and RMSD meaning ?

NB: I might also add that, weirdly enough, on the last run the best Chi2 model is actually completely not superimposable with the SAXS DAMMIF shape whereas the one with the best RMSD is... :shock:
by Nyshae
2017.02.07 10:54
Forum: Mixtures and Flexible Systems
Topic: SREFLEX Chi2 and RMSD meaning ?
Replies: 14
Views: 3956

Re: SREFLEX Chi2 and RMSD meaning ?

Hi, Thanks both for your answers, much appreciated! I'm using the ATSAS 2.8.0 version (on Mac) by the way ;) In my case, the pdb file is not an actual crystallographic structure but an atomic model based on computing and various inputs. In that case, given how you define the values, the only value t...
by Nyshae
2017.02.06 13:30
Forum: Mixtures and Flexible Systems
Topic: SREFLEX Chi2 and RMSD meaning ?
Replies: 14
Views: 3956

SREFLEX Chi2 and RMSD meaning ?

Hi everyone! I have what is maybe a super simple question: when I run SREFLEX on the online mode, I get as an output a summary files with, for each of the proposed refined models, a Chi2 value, an RMSD value and a clashes number. I just want to know: to what exactly are those values referring to? Th...
by Nyshae
2016.10.17 13:36
Forum: Rigid Body Modelling
Topic: Fitting a SASREF model and a X-ray structure
Replies: 3
Views: 4247

Re: Fitting a SASREF model and a X-ray structure

Thanks for your input! I have basically one crystallographic model of my dimer where you can only see the dimeric interface of domain As and also computed atomic models of each domain A and B separately. I am already using PyMOL to do that but I would have liked to get a program that could also issu...
by Nyshae
2016.09.28 14:45
Forum: Rigid Body Modelling
Topic: Fitting a SASREF model and a X-ray structure
Replies: 3
Views: 4247

Fitting a SASREF model and a X-ray structure

Hi all, I am working with a dimeric protein which has two domains. I made an atomic model of domain A and another for domain B (from literature data and homologous structures). I have SAXS data on the dimeric protein. Using both, I got a nice SASREF build (for the dimer). I later on got crystals of ...
by Nyshae
2015.11.11 10:33
Forum: Working with Models
Topic: Docking an atomic protein computer model in SAXS
Replies: 4
Views: 3047

Re: Docking an atomic protein computer model in SAXS

Sorry for the misunderstanding. Yes, the model represents a protein 3D structure with amino acids positions. So yes, I could try SREFLEX ! I just had the older version of ATSAS so didn't see that.
Thanks again !
by Nyshae
2015.11.10 12:36
Forum: Working with Models
Topic: Docking an atomic protein computer model in SAXS
Replies: 4
Views: 3047

Re: Docking an atomic protein computer model in SAXS

Hi,
Thanks a lot for your answers !
For question b), the model in question is purely computational (based also on literature references).
by Nyshae
2015.11.03 15:04
Forum: Working with Models
Topic: Docking an atomic protein computer model in SAXS
Replies: 4
Views: 3047

Docking an atomic protein computer model in SAXS

Hi everyone! I am working with this protein and trying to get an idea of its shape. A model has been generated by computing various parameters and the protein has also been measured in SAXS. When I fit the model vs the SAXS data (with CRYSOL) I get a fit that is not optimal but not horrible either. ...