BUNCH segmentation error

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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papiz
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Posts: 6
Joined: 2007.10.08 12:21
Location: Daresbury Laboratory

BUNCH segmentation error

#1 Post by papiz » 2007.10.08 12:47

I am running bunch8.l86 with 2 domains in the monomer and then a dimer is created from this by using P2 symmetry in bunch.

As soon as I read in the pre_bunch created pdb file and then
apply P2 symmetery it crashes with a "Segmetation fault".
I have checked that the 2-fold is along the Z axis and the dimer looks sensible when generated in Pymol. I even went to the trouble of
regularizing the domains where they join using Coot. Has anyone seen similar problems.

SaxsMax
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#2 Post by SaxsMax » 2007.10.09 18:43

Did you try to run Bunch on another platform,
in other words does only l86 version crash?

Does the sequence have a gap between the two domains
(at least 3AA gap is required)?

Could you send your output from pre_bunch to
atsas_at_embl-hamburg.de to be checked?

papiz
Member
Posts: 6
Joined: 2007.10.08 12:21
Location: Daresbury Laboratory

Bunch segmentation fault

#3 Post by papiz » 2007.10.10 13:19

Thanks for the info SaxMax. I don't have a gap between the domains I thought they had to be contiguous. If that is the case do I need to insert 3 AA in the sequence info and how do I number the AA in the PDB files do they also need a gap.

Miroslav

SaxsMax
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Posts: 349
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#4 Post by SaxsMax » 2007.10.10 21:16

Well, in fact it should be four, not three AA, sorry.
And then you need to cut out these residues from the
pdb files of the domains

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