Topics

1

DNA/RNA-protein interactions (SNAP) / Which residues does SNAP define reference frames for?

« on: August 02, 2018, 07:29:39 pm »

Hello, since there's no paper for SNAP yet (you should write one at some point!), I'm just going by my experience with the program and this forum. As I understand, pseudo-pairing and stacking interactions are identified based on geometric criteria between a planar moiety which defines the amino acid reference frame, and the standard base reference frame. So these are plane-plane interactions.

My question is, for which residues exactly are reference frames defined? Does every amino acid (perhaps except alanine and glycine) have a defined reference frame? So can any residue participate in pseudo-pairing and stacking, or does SNAP only identify these interactions for a subset of amino acids?

Thanks.

2

RNA structures (DSSR) / include non-cannonical base-pairing in DBN output?

« on: June 07, 2018, 07:15:28 pm »

Hello, is there a simple way to include include non-canonical base-pairs in the DBN output of DSSR?

Currently, it seems that non-canonical base-pairs are ignored, and those nucleotides are treated as unpaired in the DBN output. I didn't see any simple way of changing this behaviour in the manual, but was wondering if i'm missing something.

Thanks.

3

RNA structures (DSSR) / Odd output for G-quadruplex structure

« on: September 20, 2017, 02:50:41 pm »

Hi, for the structure 2chj, http://www.rcsb.org/pdb/explore/explore.do?structureId=2chj, DSSR produces some odd output.

First, it identifies two helices instead of one. This is somewhat understandable since removing two strands would still produce a helical structure, but it would be nice if DSSR could identify higher-order helices automatically. Perhaps the definition of a base-pair could be generalized to include any number of nucleotides, and helices could be defined based on the stacking of these generalized base-pairs.

Second, it identifies each strand as a single-stranded segment, which is clearly a bug. Not sure how a single-stranded segment is defined, but I'm guessing it has to do with there being no first order base pairs (i.e. one to one base pair) in the structure.

4

DNA/RNA-protein interactions (SNAP) / --cleanup option doesn't work

« on: September 24, 2016, 06:18:48 pm »

Hello, when using the linux binary, the --cleanup option doesn't work. Instead of outputting the -output='filename' file, and removing all the generated .pdb files, no output is produced at all. Surely this is not the intended behavior.

Thanks.

5

Feature requests / JSON or similar machine-readable output for 3DNA

« on: September 24, 2016, 05:30:01 pm »

Hello, it would be great to have a machine-readable output for 3DNA and indeed all the software tools in the 3DNA suite. If such an option were present, it would also be great to be able to suppress other output files.

Currently, it's very annoying to parse the 3DNA ouput files, and slight changes in the ouput format from version 2.1 to 2.3 may break scripts to do so. A machine readable format would solve this and give 3DNA a big advantage over competitors in my mind.