Trouble Looping Missing Regions For Subsequent BilboMD

Calculation of SAXS and SANS profiles (CRYSOL, CRYSON), superposition of models (SUPCOMB, DAMAVER, DAMCLUST), database DARA, PyMOL plugin SASpy
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cjuark
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Joined: 2020.02.12 05:33

Trouble Looping Missing Regions For Subsequent BilboMD

#1 Post by cjuark » 2020.09.15 21:20

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!
Attachments
2147pdb.txt
sequence file for pdb
(959 Bytes) Downloaded 15 times
02147eom.pdb
(381.4 KiB) Downloaded 21 times
colgtrunc - Copy.txt
full length FASTA sequence for protein
(975 Bytes) Downloaded 18 times

cjuark
Active member
Posts: 19
Joined: 2020.02.12 05:33

Re: Trouble Looping Missing Regions For Subsequent BilboMD

#2 Post by cjuark » 2020.09.15 21:41

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.

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