PROBLEM: The sequence presents a residue (0) not recognized

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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Julie2222
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PROBLEM: The sequence presents a residue (0) not recognized

#1 Post by Julie2222 » 2017.09.18 10:06

I get the error 'PROBLEM: The sequence presents a residue (0) not recognized' when running EOM.
All letters in the seq file are uppercase, i tried both with and without the first line in the fasta format and checked my sequence 100 times. Anyone who knows how to solve the problem? I am using MAC.

Cheers,
Julie

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Hayds
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Re: PROBLEM: The sequence presents a residue (0) not recogni

#2 Post by Hayds » 2017.09.19 15:02

Hi Julie,

can you please pm me your sequence file? Is the EOM run using any PDB files or just random structure?

Julie2222
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Re: PROBLEM: The sequence presents a residue (0) not recogni

#3 Post by Julie2222 » 2017.09.19 15:35

It is a 7 domain protein and i have used 7 different pdb structures. I had a hard time understanding which sequence the EOM actually need so i tried both with the sequence of the protein tested with SAXS and all the sequences of the pdb structures. I tried using the sequences in fasta format but naming the file seq.seq and also tried without the fasta headers.
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Hayds
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Re: PROBLEM: The sequence presents a residue (0) not recogni

#4 Post by Hayds » 2017.09.19 16:04

Hi Julie,

try removing all the non-alphabetical characters from the sequence files, you should only have something like this:

MLLAQKPFWQRHLAYPHINLDTVAHSLRLTGPLDTTLLLRALHLTVSEIDLFRARFSAQG
ELYWHPFSPPIDYQDLSIHLEAEPLAWRQIEQDLQRSSTLIDAPITSHQVYRLSHSEHLI
YTRAHHIVLDGYGMMLFEQRLSQHYQSLLSGQTPTAAFKPYQSYLEEEAAYLTSHRYWQD
KQFWQGYLREAPDLTLTSATYDPQLSHAVSLSYTLNSQLNHLLLKLANANQIGWPDALVA
LCALYLESAEPDAPWLWLPFMNRWGSVAANVPGLMVNSLPLLRLSAQQTSLGNYLKQSGQ
AIRSLYLHGRYRIEQIEQDQGLNAEQSYFMSPFINILPFESPHFADCQTELKVLASGSAE
GINFTFRGSPQHELCLDITADLASYPQSHWQSHCERFPRFFEQLLARFQQVEQDVARLLA
EPAALAATTSTRAIAS

Just plain text. Remove any spaces and "/" or "{" for example.

Let me know how it goes.

Cheers,

Haydyn

Julie2222
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Re: PROBLEM: The sequence presents a residue (0) not recogni

#5 Post by Julie2222 » 2017.09.19 16:39

I have tried that many times and it results in the same error. Can anything else give that error, when the sequence is fine?

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Hayds
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Re: PROBLEM: The sequence presents a residue (0) not recogni

#6 Post by Hayds » 2017.09.21 09:17

Hi Julie,

I just removed all the extra characters and EOM runs fine with the modified sequence file (EOM run without using any rigid bodies, just random coil from sequence).

In your case I assume you have corresponding rigid bodies. Do you have anything in the PDB files that is unusual?

Cheers,

Haydyn

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