CORAL domain configutation issues

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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jeremyk
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Posts: 11
Joined: 2012.12.16 04:28

CORAL domain configutation issues

#1 Post by jeremyk » 2016.01.12 06:55

Hi All,

I have been attempting to use the the newest version of CORAL to model the position of a missing domain.

Some background... The protein is trimeric in solution and each protomer comprises two domains with a 12 residues linker between them. I know the position of one domain from each protomer and have thus fixed this in my modelling. The second domain (for which I have atomic resolution data but it's location relative to the first domain is unknown) has been allowed to move.

I have been able to get CORAL running correctly if I do not fix the known domains;however, it fails stating "Domain 2: fixation is not compatible with initial configuration" if I try fixing the domain.

I dont think it is a problem with any of the input files as the program runs if I don't fix those domains.

Is there some limitation/constraint on the location of N-/C- termini relative to each other or something else I am over looking?

Any help would be much appreciated.

Cheers,

Jeremy

ckerr
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Joined: 2015.03.25 09:03
Location: EMBL Hamburg

Re: CORAL domain configutation issues

#2 Post by ckerr » 2016.01.12 09:35

The limit is seven Angstrom between the end of domain N and the start of domain N+1, however this only applies if domain N+1 is fixed. Presumably something is causing the second domain to be fixed although you didn't mean it to be.

jeremyk
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Posts: 11
Joined: 2012.12.16 04:28

Re: CORAL domain configutation issues

#3 Post by jeremyk » 2016.01.13 00:47

Thanks for the advice, I manually moved the unfixed domain much closer to the fixed domain and this fixed the problem.

Cheers,
Jeremy

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