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Trouble Looping Missing Regions For Subsequent BilboMD

Posted: 2020.09.15 21:20
by cjuark
Hello,

I am trying to to loop in missing regions within a single chain multidomain protein which I have previously generated a model of using EOM at my local compute cluster. I have had recent success modelling in missing loop regions of a protein using the Modeller plug in within chimera, and then used the newly modeled protein in BilboMD. Unfortunately, I am unable to fill in missing residues with another protein I am working with, and am at a complete loss as to why. Bringing up both the FASTA and pdb sequence alignment in chimera, followed by "all missing structure" selection with modeller is providing no models. Further towards the carboxy terminus of my pdb file, the numbering of the residues abruptly restarts and I am wondering if that is the reason why. Is there a fix for this other than having to manually readjust the numbering of each residue within the text file?

I have attached the pdb file, the sequence of the pdb file, and the FASTA sequence for the full length protein as a text file. Thank you!

Re: Trouble Looping Missing Regions For Subsequent BilboMD

Posted: 2020.09.15 21:41
by cjuark
On a whim, I googled "how to renumber a pdb file" and I found this website: https://swift.cmbi.umcn.nl/servers/html/renumb.html. I input the pdb I generated with EOM and magically, the output had my missing residues filled in. Highly recommend this method as it only took a few seconds.