Topics

1

RNA structures (DSSR) / dssr did not recognize some canonical nucleotide in 6nd4 chain 2

« on: October 21, 2021, 07:52:52 pm »

I am using dssr version v1.9.10-2020apr23 to analyze PDB 6nd4 chain 2. There are 146 standard nucleotides in this chain. However, when I run

x3dna-dssr -i=6nd42.pdb  -o=output.dssr

It reports
    total number of nucleotides: 144

This also causes the dssr-2ndstrs.dbn files to have 144 rather than 146 positions. It seems dssr disregard residue G248 for unknown reason.

2

RNA structures (DSSR) / dssr stdin

« on: May 30, 2020, 11:45:49 am »

Can x3dna-dssr uses stdin for input? The following flags apparent do not work (yet):
cat file.pdb | x3dna-dssr -i=stdin
cat file.pdb | x3dna-dssr -i=-
If there is source code for dssr, I am happy to help with implementing such a feature.