SAXS

Small Angle X-ray Scattering Initiative for Europe :: Forum
It is currently 2018.02.24 17:55

All times are UTC + 2 hours




Post new topic Reply to topic  [ 3 posts ] 
Author Message
PostPosted: 2018.01.23 01:26 
Offline
Member

Joined: 2017.03.06 16:37
Posts: 7
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 pentameric protein.
However, it is, to my knowledge, not possible in the online version (SASREF online), nor when running in batch mode (sasrefcv), even when running in Expert mode.

Is there a way to do this?

Best regards,
Andreas


Top
 Profile  
 
PostPosted: 2018.02.05 14:28 
Offline
Administrator
User avatar

Joined: 2007.08.03 18:55
Posts: 616
Location: EMBL Hamburg, Germany
Increasing the number of harmonics in SASREF is technically challenging. It is not planned to release a version of SASREF/CV/MX with more than 15 harmonics in the nearest future.
You may try to shorten the fitting range to see if this improves the modelling. Use constant subtraction.
You may do multiple SASREF CV runs, then fit the resulting models to the experimental data using CRYSOL/CRYSON with 50 harmonics and pick the best fitting model.


Top
 Profile  
 
PostPosted: 2018.02.08 15:40 
Offline
Member

Joined: 2017.03.06 16:37
Posts: 7
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 other projects) and limited time! (However, if it was open source someone else might dig into it ;-) )... You could maybe consider implementing a warning/disclaimer, if a large protein is given as input combined with a large q-values in the input data...

FYI: A really minor thing, but it says in the SASREF manual (and the SASREF CV/MX manual) that the default minimum # of successes to continue is 50 * total number of subunits. I am running with 5 subunits with default values, but the program prints a value of 100. So either the manual, or the print-statement, or the program itself needs an update to be consistent... Probably the manual, I guess...?

Best regards,
Andreas


Top
 Profile  
 
Display posts from previous:  Sort by  
Post new topic Reply to topic  [ 3 posts ] 

All times are UTC + 2 hours


Who is online

Users browsing this forum: No registered users and 1 guest


You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot post attachments in this forum

Search for:
Jump to:  
Powered by phpBB® Forum Software © phpBB Group