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.
How to use EOM on glycosylated proteins
GLYCOSYLATION
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.
Re: How to use EOM on glycosylated proteins
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
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
Re: How to use EOM on glycosylated proteins
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?
Re: How to use EOM on glycosylated proteins
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
It only runs if I dont specify the glycans at all. It still complaints of mismatch
Re: How to use EOM on glycosylated proteins
Any idea if this can be solved?
Re: How to use EOM on glycosylated proteins
Hi,
the trick to do this is to add the GLYCANS (using the GLYCOSYLATION ATSAS toll for example), but to then split the PDB files of the protein and the attached glycan. Then when EOM asks if there is 'bound DNA' for each rigid body you then provide the glycan PDB file.
Let us know how this works for you.
Cheers,
Haydyn
the trick to do this is to add the GLYCANS (using the GLYCOSYLATION ATSAS toll for example), but to then split the PDB files of the protein and the attached glycan. Then when EOM asks if there is 'bound DNA' for each rigid body you then provide the glycan PDB file.
Let us know how this works for you.
Cheers,
Haydyn