Search found 24 matches

by Nyshae
2017.11.06 11:28
Forum: Mixtures and Flexible Systems
Topic: EOM input bug (shell version)?
Replies: 2
Views: 4679

Re: EOM input bug (shell version)?

Hi,
Yes, it is the case. I didn't realize it would be a problem, thanks for the input!
by Nyshae
2017.11.01 12:51
Forum: Mixtures and Flexible Systems
Topic: EOM input bug (shell version)?
Replies: 2
Views: 4679

EOM input bug (shell version)?

Hi all, I like to use the shell version of EOM because it's telling me about the problems right away... However, there seem to have a bug (or I'm really dumb)... My setup: Mac OS Sierra, finnish keyboard (qwerty with extra letters), ATSAS 2.8.2 version My problem: at this line of input: Contacts fil...
by Nyshae
2017.11.01 12:45
Forum: Mixtures and Flexible Systems
Topic: EOM as a dimer with no PDBs
Replies: 2
Views: 4407

Re: EOM as a dimer with no PDBs

You can do that only if your protein is intrinsically unfolded. If it is just that you don't know the structure (but it still has one), you might either want to use models based on your sequence and a homolog structure (made for example with SWISS model) or use another program (e.g. DAMMIN-F).
by Nyshae
2017.10.19 12:56
Forum: Rigid Body Modelling
Topic: SASREF Distance constraint
Replies: 2
Views: 6895

Re: SASREF Distance constraint

Hi Claudia, I'm by no means an expert here but just a regular user so I'll try to see if I can help a bit ;) You can check SASREF manual there: https://www.embl-hamburg.de/biosaxs/manuals/sasref.html About your questions: -the distance you input is a maximum (so it can be shorter) so in your case yo...
by Nyshae
2017.10.02 10:06
Forum: Mixtures and Flexible Systems
Topic: EOM - Using two models with internal P2 symmetry
Replies: 12
Views: 7669

Re: EOM - Using two models with internal P2 symmetry

Hi AL, So I managed to do what you suggested and it worked very nicely! My Chi2 is not super good (around 9) and the fit is not either but it seems much better than previously! I suspect the "not super goodness" might be due to the fact that the frames I used are not 100% monodisperse (I used CORAL ...
by Nyshae
2017.09.28 16:15
Forum: Mixtures and Flexible Systems
Topic: EOM - Using two models with internal P2 symmetry
Replies: 12
Views: 7669

Re: EOM - Using two models with internal P2 symmetry

So after verification, the dimer is 106 kDa. There is indeed another peak, suspected tetramer (212 kDa). They unfortunately do overlap a little bit... I tried to select and average the frames that had a stable Rg (rather the end of the dimer peak), I hope it's enough... Thanks a lot for your suggest...
by Nyshae
2017.09.28 09:25
Forum: Mixtures and Flexible Systems
Topic: EOM - Using two models with internal P2 symmetry
Replies: 12
Views: 7669

Re: EOM - Using two models with internal P2 symmetry

Thanks for the reply! Well actually each monomer is around 52 kDa + 4 glycosylations and on MALS it runs as a 106-120 kDa species (I don't have the precise weight right now, it's another persons' part). So, smaller than what you say... How did you get the 200? We think it might be somewhat flexible ...
by Nyshae
2017.09.25 14:31
Forum: Rigid Body Modelling
Topic: Coral Restrains chain ID problem
Replies: 9
Views: 8401

Re: Coral Restrains chain ID problem

Actually, my apologies, I did many trials and got lost in the file piles, the actual constraint penalty is around 27-29 (the 0 one is the one where I tried without constraints).
by Nyshae
2017.09.25 11:44
Forum: Mixtures and Flexible Systems
Topic: EOM - Using two models with internal P2 symmetry
Replies: 12
Views: 7669

Re: EOM - Using two models with internal P2 symmetry

Hi, I thought I would be ok to continue your topic since I'm encountering a sort-of similar issue. I have a protein composed of 3 domains. We know it forms dimers in solution and we suppose it's through domain A (it is the case in proteins of the same family which we have structure from). We have SE...
by Nyshae
2017.09.25 11:36
Forum: Rigid Body Modelling
Topic: Coral Restrains chain ID problem
Replies: 9
Views: 8401

Re: Coral Restrains chain ID problem

Sorry about the time lapse, I don't come so often ^^'

best Chi2 values: 3,6643
contact penalty: 0,00000
by Nyshae
2017.08.31 14:49
Forum: Rigid Body Modelling
Topic: Coral Restrains chain ID problem
Replies: 9
Views: 8401

Re: Coral Restrains chain ID problem

Hi, Thanks for the tip! I managed since then to find out a working set of constraints (at least the program accepts it) that do resemble yours. Now I have another problem... : I basically have a protein dimer which is in an anti-parallel way. So I input P2 symmetry and a set of constraints to have e...
by Nyshae
2017.06.07 10:41
Forum: Rigid Body Modelling
Topic: Coral Restrains chain ID problem
Replies: 9
Views: 8401

Re: Coral Restrains chain ID problem

Hi, I thought I would just resuscitate this post because I have a similar issue... My setup is the following: one protein = domain A + short linker + domain B. The protein forms a dimer and we do know (from crystallographic data) that the domains A are dimerizing. I want to set CORAL with the pdbs o...
by Nyshae
2017.04.03 16:09
Forum: Working with Models
Topic: Plotting CRYSOL fits with another software
Replies: 2
Views: 5260

Re: Plotting CRYSOL fits with another software

Many thanks! I have a nice plot now ^^
by Nyshae
2017.04.03 14:37
Forum: Working with Models
Topic: Plotting CRYSOL fits with another software
Replies: 2
Views: 5260

Plotting CRYSOL fits with another software

Hi, Again, it might be a simple question but I can figure out how to do it... I have run CRYSOL for fitting different models to my data. I have my fits and all the output files. When I open the .fit files with SASPLOT, I have a nice graph. However, I would like to re-plot it using eg excel or prism....