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@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@simtk.org https://simtk.org/mailman/listinfo/rnatoolbox-help