I surveyed the capability of pdbrx to work on missing residues in nucleic acid.
1, pdbrx generated clean output pdb and psf files for double stranded dna (5ju4.pdb)
5ju4.pdb.gz with HET atoms in default mode.
pdbrx default mode worked well with single stranded dna without HET atoms.
single_strand.pdb.gz.
I added 3 missing residues at the end of the model single strained dna
single_strand_missing.pdb.gz. The default mode ran without error but pdbrx didn't add the missing residues.
Run in non-default mode failed to read input fasta file (CGTGAATTCACGggg) with an error as below.
####################################################################
Enter filename containing FASTA sequence for segment A: fasta.txt
Traceback (most recent call last):
File "gui_mimic.py", line 42, in
scan.main(variables,txtQueue)
File "/home/cjeong/Nucleotide_pdbrx_results/5JU4/pdbrx/pdb_rx.py", line 59, in main
self.run_scan()
File "/home/cjeong/Nucleotide_pdbrx_results/5JU4/pdbrx/pdb_rx.py", line 120, in run_scan
preprocessor.user_edit_options()
File "/home/cjeong/Nucleotide_pdbrx_results/5JU4/pdbrx/pdbrx/preprocessor.py", line 738, in user_edit_options
self.terminal_edit_options()
File "/home/cjeong/Nucleotide_pdbrx_results/5JU4/pdbrx/pdbrx/preprocessor.py", line 674, in terminal_edit_options
segname, fasta_sequence)
File "/home/cjeong/Nucleotide_pdbrx_results/5JU4/pdbrx/pdbrx/preprocessor.py", line 468, in complete_sequence_fasta
resid = first_resid + position
I surveyed the capability of pdbrx to work on missing residues in nucleic acid.
1, pdbrx generated clean output pdb and psf files for double stranded dna (5ju4.pdb) 5ju4.pdb.gz with HET atoms in default mode.
pdbrx default mode worked well with single stranded dna without HET atoms. single_strand.pdb.gz.
I added 3 missing residues at the end of the model single strained dna single_strand_missing.pdb.gz. The default mode ran without error but pdbrx didn't add the missing residues. Run in non-default mode failed to read input fasta file (CGTGAATTCACGggg) with an error as below.
#################################################################### Enter filename containing FASTA sequence for segment A: fasta.txt Traceback (most recent call last): File "gui_mimic.py", line 42, in
scan.main(variables,txtQueue)
File "/home/cjeong/Nucleotide_pdbrx_results/5JU4/pdbrx/pdb_rx.py", line 59, in main
self.run_scan()
File "/home/cjeong/Nucleotide_pdbrx_results/5JU4/pdbrx/pdb_rx.py", line 120, in run_scan
preprocessor.user_edit_options()
File "/home/cjeong/Nucleotide_pdbrx_results/5JU4/pdbrx/pdbrx/preprocessor.py", line 738, in user_edit_options
self.terminal_edit_options()
File "/home/cjeong/Nucleotide_pdbrx_results/5JU4/pdbrx/pdbrx/preprocessor.py", line 674, in terminal_edit_options
segname, fasta_sequence)
File "/home/cjeong/Nucleotide_pdbrx_results/5JU4/pdbrx/pdbrx/preprocessor.py", line 468, in complete_sequence_fasta
resid = first_resid + position