I'm trying to run EOM with a dimeric protein that has one dimeric ordered domain (P2 symmetry, fixed domain, "oligomeric" selected, the dimeric assembly is defined in the pdb file) that is flanked by disordered regions. I'm running it on the ATSAS server and I get this error:
ERROR: Unknown residue ( ) detected.
Preceding sequence: M ... G[ ]
In the .seq file that last G is the final protein residue and also the final character in the text file. There is no space, break, symbol or anything else after it. The strange part is that I used the exact same sequence file to successfully run another EOM run with different input models, although that one halts also but for different reasons.
Also: if someone has any practical suggestion how to run EOM on a dimeric protein that has two dimeric domains interconnected by linkers, where one domain "block" is fixed and the other domain block is moving in respect to the other, I would highly appreciate that. The closest example I could find would be shown in Fig 3 of https://www.nature.com/articles/ncomms10355. Essentially the same situation but in addition both monomers have a C-terminal tail which is roughly 100 amino acids in length.
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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