EOM of dimer with missing loops

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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jvakonakis
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Posts: 3
Joined: 2013.03.14 18:42

EOM of dimer with missing loops

#1 Post by jvakonakis » 2018.11.09 15:43

Dear all,

I am trying to model a homodimeric protein using EOM. We have the crystallographic structure of the homodimer but it misses residues at both the N- and C-termini of each chain, as well as in an internal loop. I've tried running EOM providing the chain sequence (one copy of the chain in the sequence file) and a single PDB file of the homodimer described above but encounter the "Alignment Problems: check the sequence and the domains" error. When splitting the PDB file in two parts, each containing a fraction of the homodimer up to the point of the missing loop, EOM starts running but aborts after a few seconds with the error "not possible to continue on making the pool. Please check the input files". Do I need to split the PDB into 4 files (single chains and only part of the domain in each) and, if so, how can I impose P2 symmetry?

Thanks in advance for any help.

John

jmarie
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Posts: 15
Joined: 2009.01.12 10:55
Location: IBCP,france

Re: EOM of dimer with missing loops

#2 Post by jmarie » 2018.11.12 11:50

Hi
Did you see this post
viewtopic.php?f=10&t=3822&hilit=eom+dimer+of+dimers

It might help you
Cheers
JM

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