SASREF Distance constraint

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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geoX
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Posts: 4
Joined: 2015.12.09 17:49

SASREF Distance constraint

#1 Post by geoX » 2016.06.05 12:50

Hi

I wanted to specify a distance constraint in SASREF covering a certain range. I found in a previous post that you can use "drng min_dist max_dist" to specifiy minimum and maximum distance restraints what would be exactly what I am looking for. Is there an "official" reference to this command somewhere? I couldn't find it in the online manual.

Thanks
Georg

Claudia Kielkopf
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Joined: 2017.10.11 23:44

Re: SASREF Distance constraint

#2 Post by Claudia Kielkopf » 2017.10.12 00:15

Dear Saxiers,

I would like to revive this post since I have a very similar problem.
I want to use Sasref online (SASREF07) to model my tetramer from the published monomer crystal structure. To restrain the modelling, we performed crosslinking mass spec using BS3 as crosslinker which has a length of 11.4A when fully extended, allowing a maximum distance between C alpha atoms of ~30A. A publication has shown, however, that the real distance can be smaller.
How can I incorporate this in sasref online? Is the number I put in for "Interresidue distance: Å between..." a fixed number or a maximum distance? If it's a fixed number, do I then need to run several runs and change the restraint in each run?

In case sasref online isn't suitable for my case, can I use the local sasref installation (ATSAS 2.8.2) for modelling? How exactly would I do that, since for creating the contact file I enter the same information as in sasref online?

Thanks very much for any help!

Cheers,
Claudia

Nyshae
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Posts: 24
Joined: 2015.11.03 14:38

Re: SASREF Distance constraint

#3 Post by Nyshae » 2017.10.19 12:56

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 you don't need to run it several times
-for running SASREF locally you need to be a bit familiar with the basics of the kernel/LINUX environment. Open a terminal window, decide of your folder destination and just use the command "sasref". The rest is in dialog mode. You can check the manual on how to answer. You will need as input: your data (in .dat), your atomic model (in .pdb), some information (aka coupling, symmetry, etc) and a potential contact constraints file (in .cnd, you can make it with a text editor).

Hope it can be of use!

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