Messages

1

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

« on: October 22, 2021, 02:40:45 pm »

This is probably misleading. For the sake of calculating base pairs, I completely agree that we should not consider nucleobases with highly distorted conformation. However, when counting how many nucleotides are there in the sequence (e.g., when generating ct or dbn files), nucleotides with distorted base conformation (or even nucleotides without their base groups) are still nucleotides. It may not be a good idea to just delete them from the sequence without at least printing out a warning message.

2

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.

3

RNA structures (DSSR) / Re: dssr stdin

« on: June 08, 2020, 03:51:39 pm »

Yes, stdin works, thank you. It will be good if this feature is documented in the program.

4

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.