CORAL - parameters for initial configuration

Global minimization programs: SASREF, CORAL, BUNCH, GLOBSYMM
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CORAL - parameters for initial configuration

#1 Post by Wouter » 2022.10.18 15:56

Dear SAXS aficionados,

I am using CORAL on a relatively complex configuration, consisting of two chains with 8-10 domains each.
I would like to use domain grouping and fixation to include everything we know based on biochemistry/cryo-EM/AlphaFold.

However, I am consistently running into errors such as: "Domain X: fixation/grouping is not compatible with initial configuration".
I have tried moving domains around and removing domains or putting them in PDBs as one unit and this has sporadically resulted in a job that would work.
I have read on this forum that apparently rules do exist for the initial configuration regarding distances between termini and linker lengths, but I have not been able to find these in the documentation or anywhere else.

Does anyone have an idea what sort of restrictions there are on the initial configuration that are required for grouping/fixation?


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Re: "Domain X: fixation/grouping is not compatible with initial configuration"

#2 Post by AL » 2022.11.11 18:07

I guess you are using CORAL online.
Here is the "offline" CORAL manual.
Indeed if you have "fixed" domains they have to be positioned such that the distance between them is not longer than the longest linker connecting these domains. I guess the same applies to "grouping". You may use the command line tool CIFOP to move the domains around.

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