How to use EOM on glycosylated proteins

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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Loki03
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How to use EOM on glycosylated proteins

#1 Post by Loki03 » 2019.04.20 12:08

Hello,
I am new to EOM and would like to ask how to use it for glycosylated proteins? I havent found a way to add the glycosylation into the .seg file.
Thank you for any suggestions.

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AL
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GLYCOSYLATION

#2 Post by AL » 2019.04.25 14:42

Loki03 wrote:
2019.04.20 12:08
I havent found a way to add the glycosylation into the .seg file.
If you mean the sequence file - this wouldn't work.
You may add glycan groups to your structured domains with the ATSAS command-line program GLYCOSYLATION.

Loki03
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Re: How to use EOM on glycosylated proteins

#3 Post by Loki03 » 2019.04.25 20:04

Thank you AL.

Can I then run it in EOM? I tried to run it on my machine but it still asks for a sequence and then doesnt match it to the pdb that I glycosylated with the GLYCOSYLATION program.
Thanks

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Re: How to use EOM on glycosylated proteins

#4 Post by AL » 2019.04.30 10:30

Loki03 wrote:
2019.04.25 20:04
... it still asks for a sequence and then doesnt match it to the pdb that I glycosylated with the GLYCOSYLATION program.
So EOM runs fine with your domain(s) an the sequence before you run GLYCOSYLATION but after you run GLYCOSYLATION it says the sequence doesn't match?

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Re: How to use EOM on glycosylated proteins

#5 Post by Loki03 » 2019.04.30 16:15

It doesn't match with the sequence file - my pdb with glycosylation added by a different software or with glycosylation added by the GLYCOSYLATION.
It only runs if I dont specify the glycans at all. It still complaints of mismatch

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Re: How to use EOM on glycosylated proteins

#6 Post by Loki03 » 2019.05.12 18:25

Any idea if this can be solved?

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