files from another job e.g., 614e0a1b
The raw output files for each step of the pipeline can be found here and downloaded as a ZIP file here.
The output are files with "_mutate.pdb".
Load the example, Click analyze to see
>X:42-44 UGCand then type into field "X:42a" and click Mutate to mutate first U into A. Run Analyze again to see if the change was introduced:
# missing_op1op2_r43OK >X:42-44 UGC # missing_op1op2_r43OK_mutate >X:42-44 AGCyes, it was, the sequence for "_mutate.pdb" output file is now AGC.
This tool works on multiple chains; for example, use 'A:1A,B:13A' to mutate the first residue of chain A into adenine and the first residue of chain B into adenine.
This is https://rna-tools.readthedocs.io/en/latest/want.html?mutate-residues#mutate-residues
The rna-tools (RNA-Puzzles toolkit) package uses ModeRNA to introduce single or double mutations in structures. But it overcomes ModeRNA’s limitation in processing only one chain at the time. Multiple mutations in multiple chains can be introduced.
M. Magnus, M. Antczak, T. Zok, J. Wiedemann, P. Lukasiak, Y. Cao, J. M. Bujnicki, E. Westhof, M. Szachniuk, and Z. Miao, “RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools.,” Nucleic Acids Research, vol. 48, no. 2, pp. 576–588, Jan. 2020.
M. Rother, K. M. Rother, T. Puton, and J. M. Bujnicki, “ModeRNA: a tool for comparative modeling of RNA 3D structure.,” Nucleic Acids Research, vol. 39, no. 10, pp. 4007–4022, May 2011.
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