Coral in ATSAS 2.6.0-1:Problems grouping and fixing domains

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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Andrew
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Coral in ATSAS 2.6.0-1:Problems grouping and fixing domains

#1 Post by Andrew » 2015.03.17 00:45

I have set up a coral run with 6 domains and I want to correlate the movement of domains of 1 with 3 and 2 with 4. Everytime I came up with an error message "groupping is not compatible with initial configuration". In trying to find the problem with my input files I also tried fixing domains, but this yielded the error message "fixation is not compatible with initial configuration".

I spent a great deal of time trying to find my problem, but as soon as I moved back to the version of Coral in ATSAS 2.5.2-1 everything worked perfectly. Is there any reason for the difference in behaviour for the two versions?

Andrew
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Joined: 2009.01.28 00:06

Re: Coral in ATSAS 2.6.0-1:Problems grouping and fixing doma

#2 Post by Andrew » 2015.03.17 06:38

It appears to be all due to the length of the linkers. The distance between the N- and C- termini of adjacent subunits must be greater than some specified maximum distance for linkers of a given length.

All domains came from positions in a crystal structure, and I removed sections of loop between subunits and called them linkers. These linkers ranged in length from 6-9 AA and this caused problems. When I arbitrarily changed the length of all linkers to 9 AA, everything worked fine. This is not ideal, but at least I understand why it wasn't working.

rosepolaris
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Re: Coral in ATSAS 2.6.0-1:Problems grouping and fixing doma

#3 Post by rosepolaris » 2015.10.06 21:10

Thanks to your post, I was able to get Coral running.
For me, a linker of 6 AA is enough.

ATSAS 2.6

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