Messages

1

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

« on: August 06, 2018, 03:40:00 pm »

Great, thanks for the info!

2

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.

3

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

« on: June 08, 2018, 02:04:30 pm »

Thanks, I was just wondering if there was a quick solution - my use case is quite specific, but it relates to visualization. I believe I can just parse the .ct output and generate my own DBN fairly easily.

4

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.

5

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.

6

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

« on: October 11, 2016, 07:25:15 pm »

Yup, everything seems to be fixed. Thanks for the prompt response!

7

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

« on: September 26, 2016, 04:26:10 pm »

Here's the exact output and behaviour I get.

Code: [Select]

$ ls
1jgg.pdb
$ x3dna-snap -i=1jgg.pdb -o=1jgg-snap.out

Processing file '1jgg.pdb' [1jgg]
    total number of base pairs: 10
    total number of helices: 1

Time used: 00:00:00:00
$ ls
1jgg.pdb       AT-asn.pdb  A-val.pdb        snap-dssp.txt         T-asn.pdb
1jgg-snap.out  AT-gln.pdb  C-tyr.pdb        snap-helices.pdb      T-gln.pdb
A-arg.pdb      AT-lys.pdb  G-arg.pdb        snap-pairs.pdb        T-lys.pdb
A-asn.pdb      AT-met.pdb  GC-arg.pdb       snap-po4AA.pdb        T-met.pdb
A-gln.pdb      AT-tyr.pdb  GC-tyr.pdb       snap-pseudoPairs.pdb  T-tyr.pdb
A-met.pdb      AT-val.pdb  G-tyr.pdb        snap-sugarAA.pdb      T-val.pdb
AT-arg.pdb     A-tyr.pdb   snap-baseAA.pdb  T-arg.pdb
$ x3dna-snap --cleanup
done with cleaning up files.

Time used: 00:00:00:00
$ ls
1jgg.pdb       A-met.pdb   AT-met.pdb  C-tyr.pdb   T-arg.pdb  T-tyr.pdb
1jgg-snap.out  AT-arg.pdb  AT-tyr.pdb  G-arg.pdb   T-asn.pdb  T-val.pdb
A-arg.pdb      AT-asn.pdb  AT-val.pdb  GC-arg.pdb  T-gln.pdb
A-asn.pdb      AT-gln.pdb  A-tyr.pdb   GC-tyr.pdb  T-lys.pdb
A-gln.pdb      AT-lys.pdb  A-val.pdb   G-tyr.pdb   T-met.pdb
$ x3dna-snap --version
    SNAp: a program for the characterization of three-dimensional
             Structures of Nucleic Acid-Protein complexes
              beta-r08-2016jun02, by xiangjun@x3dna.org

  This program is being actively maintained and developed. As always,
  I greatly appreciate your feedback! Please report all SNAP-related
  issues on the 3DNA Forum (forum.x3dna.org). I strive to respond
  *promptly* to *any questions* posted there.

Time used: 00:00:00:00

As you can see, most of the PDB files are left behind. I'm using the linux binary on linux Mint 17.

8

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

« on: September 25, 2016, 06:13:43 pm »

I see - two things were unclear.

First, I thought you could run x3dna-snap in the following way:

`x3dna-snap -i=[inputfile] -o=[outputfile] --cleanup`

which, *I assumed* would produce the output files, minus whatever --cleanup removed. From your response it seems that the intended use would instead be,

`x3dna-snap -i=[inputfile] -o=[outputfile]`
`x3dna-snap --cleanup`

I was hoping that the --cleanup option would also remove ALL the generated .pdb files, including the ones which show the specific residue-nucleotide interactions. Maybe this could be considered for a future release?

Thanks for the response.

9

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.

10

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.