[RNABuilder-help] RNA threading problem

[Samuel Flores]

Sorry your message was stuck waiting for approval because of the attachment size.  I've now increased the limit to 1000 kB.

I think I have solved about 80% of your problem.  Since several residues were represented only by their "P" atoms, MMB was probably not able to match structure.  I have deleted these incomplete residues.  I also added a model of chain "X" as an extended chain (I can do this by doing a stage 1 MMB run).  I then used "loadSequencesFromPdb," which reads sequences and residue numbers directly from last.1.pdb, and tolerates missing residues (as long as the remaining residues have all their backbone atoms).  

I adjusted the "threading" command to not thread the missing residues.  I fixed chain A to the Ground frame (rootMobilizer A Weld). Lastly, I turned on the Amber99 potential for chain X only (with setDefaultMDParameters and "includeAllNonBondAtomsInResidues X 57 91").  

So now, the only part not threaded is the span from residue 71 to 81.  If you want to thread to the "P" atoms from those residues in chain A, I suggest creating eleven "springToGround" commands, connecting the  P atoms on chain X to the locations of the P atoms on chain X.  Look at the reference guide for the springToGround syntax.  You may want a nice strong spring constant, e.g. 300 or more.

Let me know how you do with the last part.  I have attached my commands.dat and last.1.pdb.

Sam


> Dear MMBians,
> 
> I am trying to thread around a section (nucleotides 57-91) of wheat 18S ribosomal RNA (3IZ7) using MMB_2.13. For some reason, instead of a hairpin I always get a straight helix. Strangely the target PDB file which is set rigid also becomes a linear molecule in the resulting PDB output. Can someone help me trouble shoot? I am attaching the command file, target pdb model and output pdb for you to see.
> 
> Target pdb chain A:
> 3IZ7-57-91.pdb
> 
> Command file threaded chain X:
> commands.3IZ7-threading-57-91.dat
> 
> Result PDB:
> Sbi-16S-57-91
> 
> I appreciate your time and input,
> 
> Uzay Sezen
> 
> Uğur Uzay Sezen
> Post-Doctoral researcher
> Plant Genome Mapping Laboratory
> University of Georgia
> Center for Applied Genetic Technologies
> 111 Riverbend Rd., Athens, GA 30602
> uzay at uga.edu
> tel: 706-583-0170
> fax: 706-583-8120
> http://www.plantgenome.uga.edu/ 
> http://naturedocumentaries.org/
> <3Iz7-57-91.pdb><commands.3iz7-threading-57-91.dat><Sbi-16S-57-91.pdb>_______________________________________________
> Rnatoolbox-help mailing list
> Rnatoolbox-help at simtk.org
> https://simtk.org/mailman/listinfo/rnatoolbox-help


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