Messages

1

General discussions (Q&As) / Re: How does 3DNA calculate rise

« on: July 03, 2019, 04:10:05 am »

Hi Xiang-Jun,

I found this definition regarding rise in the Calladine 1995 JMB paper:

Rise, Dz , is simply the component along the global
helix axis of the vector joining the mid points of
successive C6-C8 lines.

Is it calculated the same way in 3DNA ?
Sorry, I am not good at looking at the code.

Best,

Pascal

2

General discussions (Q&As) / How does 3DNA calculate rise

« on: May 21, 2019, 05:07:44 am »

Hi Xiang-Jun,

I just have a silly question but I am unable to
find a simple description of how you calculate the rise values
and, incidentally, all other values.

Thanks,

Pascal

3

Feature requests / Z-steps

« on: September 28, 2017, 12:04:38 pm »

Hi Xiang-Jun,

I am not sure since I havent' checked 3DNA pages for a while
if you implemented a feature to detect Z-steps in RNA and DNA systems
as defined in:
(if not, I think it would be nice to have and probably pretty easy to do for you).

Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops.
D'Ascenzo L, Leonarski F, Vicens Q, Auffinger P.
RNA. 2017 Mar;23(3):259-269. doi: 10.1261/rna.059097.116. Epub 2016 Dec 20.

and

'Z-DNA like' fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response.
D'Ascenzo L, Leonarski F, Vicens Q, Auffinger P.
Nucleic Acids Res. 2016 Jul 8;44(12):5944-56. doi: 10.1093/nar/gkw388. Epub 2016 May 5.

Thanks for your reply,

All the best,

Pascal

4

General discussions (Q&As) / how is Z-DNA detected by 3DNA and DSSR

« on: November 16, 2015, 07:46:35 am »

Hi Xiang-Jun,

We are wondering about how you assigne Z-DNA in your programs.
Will your programs find all Z-DNA fragments even in single strands ?
Furthermore, we wonder about the very specific orientation of the sugars
in Z-DNA CpG motifs. There, the two O4' atoms are pointing one towards the other
(see attached figure). Is there a specific parameter attached to this
type of sugar configuration in your program outputs ?
Thanks for your reply.

Best,

Pascal

5

RNA structures (DSSR) / Re: possible issue with capping interaction

« on: February 15, 2015, 10:32:58 am »

Thanks for the reply Xiang-Jun.

Can this be parametrized ? That would be nice
since I would prefer no offset.
Also, how much is that offset ?

Best,

Pascal

6

RNA structures (DSSR) / possible issue with capping interaction

« on: February 14, 2015, 11:16:22 am »

Hi Xiang-Jun,

I came across this particular capping interaction where
the O4' that is supposed to be stacked over a G is slightly off
the five membered ring. Is that expected since I thought
that such interactions were strictly above the base.

Please see attached figure.

This is the dssr output line:

****************************************************************************
List of 5 atom-base capping interactions
    dv: vertical distance of the atom above the nucleotide base
    -----------------------------------------------------------
     type       atom                 nt             dv
   1 sugar      O4'@..M.G.167.       ..M.G.166.     3.36

Best,

Pascal

7

General discussions (Q&As) / Re: Frame_mol issue with DG

« on: October 09, 2014, 12:00:19 pm »

Hi Xiang-Jun,

Sorry to have taken your time with this.
The bug was obviously on my side.
During editing, one line got corrupted in my scripts.

Best,

Pascal

8

General discussions (Q&As) / Re: Frame_mol issue with DG

« on: October 08, 2014, 12:27:40 pm »

Hi Xiang-Jun, will do that tomorrow.
I added 8 files to the mail.
did you get all of them ?

Best,

Pascal

9

General discussions (Q&As) / Frame_mol issue with DG

« on: October 08, 2014, 09:46:17 am »

Hi Xiang-Jun,

I don't know if we did something wrong but I got the impression that Frame_mol is handling in a weird manner DG nucleotides.
This means that although all other DNA or RNA nucleotides align well, DG does not.

Here are some files for checking.
and the command line

frame_mol -$numan ref_frames.dat $nucleo_filepath.base.pdb $nucleo_filepath.base.pdb

I checked the variables.

Can you check on your side ?

Best,

Pascal

10

General discussions (Q&As) / Re: small requests

« on: July 21, 2014, 02:35:24 am »

Hi Xiang-Jun,

I will use --silent, thanks for this. May be this option could be mentioned in the help file (-h).

Fot the second point:

in dssr, you have

 ****************************************************************************
List of 12 additional files
   1 dssr-stems.pdb -- MODEL/ENDMDL delineated stems
   2 dssr-helices.pdb -- MODEL/ENDMDL delineated helices (pseudo/coaxial)
   3 dssr-pairs.pdb -- MODEL/ENDMDL delineated base pairs
   4 dssr-multiplets.pdb -- MODEL/ENDMDL delineated multiplets
   5 dssr-hairpins.pdb -- MODEL/ENDMDL delineated hairpin loops
   6 dssr-4pas.pdb -- MODEL/ENDMDL delineated loop/turn interactions for Pascal
   7 dssr-2ndstrs.bpseq -- secondary structures in bpseq format
   8 dssr-2ndstrs.ct -- secondary structures in connect format
   9 dssr-2ndstrs.dbn -- secondary structures in dot-bracket notation
  10 dssr-torsions.txt -- Backbone torsion angles and suite names
  11 dssr-Uturns.pdb -- MODEL/ENDMDL delineated U-turn motifs
  12 dssr-a2bases.pdb -- MODEL/ENDMDL delineated atom-base stacking interactions

at the end of the output file. I was suggesting adding such a feature that would provide easier to
read/parse outputs.
This could be useful also in find_pair for example but seems particularly important in Snap that is a new program.

I suggest to include the line appearing on the screen (saying that the structure contains less than 5 amino acids) in the output of dssr.

Best,

Pascal

11

General discussions (Q&As) / small requests

« on: July 20, 2014, 01:36:59 pm »

Dear Xiang-Jun,

1) I would appreciate a --silent option since I am running your programs on a large number of files.

2) with snap, I would appreciate a count of the files that are written out by your program and something like a zero output file message if they are no proteins processed. This would be helpful for parsing (I know that there is a screen message, but writing it in the output file should be interesting).

Thanks for considering this if you have time.

Best,

Pascal

12

Feature requests / Re: op1_op2. request for an option to keep the pdb header

« on: June 26, 2014, 06:11:08 pm »

OK Xiang-Jun, thanks.

Its difficult to know if this means a lot of work for you or if its easy to fix.
It might have been useful to others (or not)
especially since PDB will not be quick at fixing this or will not fix it at all.
Anyway, I will figure something out and surely let them know.

Best,

Pascal

13

Feature requests / op1_op2. request for an option to keep the pdb header

« on: June 26, 2014, 01:25:24 pm »

Dear Xiang-Jun,

I was for a whole no longer using op1_op2 since I thought that the PDB
had taken care of the wrong anionic oxygen attributions.
That was assuming a little too mach and such misattributions are still found in the PDB.
(see for exemple residue 625 chain 0 in 4HUB that interacts through its N3 with the "OP1" of a m1A - should be OP2).
(other examples can be found)

Thus using op1_op2 seems still mandatory.
Yet, we stopped using it also because it gets rid of some parts of the header, especially
those that describe symmetry operations.

I such I kindly ask for a version with a -header option that would keep the original header
for those who need it.

Best,

Pascal

14

DNA/RNA-protein interactions (SNAP) / Re: interaction code and other issues

« on: June 02, 2014, 01:23:45 pm »

OK Xiang-Jun,

So when can the RNA-protein version be expected ?

Best,

Pascal

15

DNA/RNA-protein interactions (SNAP) / Re: interaction code and other issues

« on: June 02, 2014, 11:17:52 am »

Hi Xiang-Jun,

I use the  following options:
x3dna-snap --long-idstr --segid --cutoff=3.5 --hbond_d2=3.5 -i=xxx -o=yyy

It works fine for a lot of files including 4LT5
Yet could you check 1JJ2 or 1FFK that are ribosomes ?

here is my output file

****************************************************************************
    SNAP: a program for the characterization of three-dimensional
             Structures of Nucleic Acid-Protein complexes
        beta-r02-2014may31, Xiang-Jun Lu (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.

****************************************************************************
Note: Each nucleotide/amino-acid is identified by model:chainId.name#, where
      the 'model:' portion is omitted if no model number is available (as is
      often the case for x-ray crystal structures in the PDB). So a common
      example would be B.DA1689, meaning adenosine #1689 on chain B.

Command: x3dna-snap -i=/media/HD/DATA/pdb_files_temp/1FFK/1FFK.py.pdb -o=1FFK.py.snap.3.5.out --cutoff=3.5
Date and time: Mon Jun  2 15:32:22 2014
File name: 1FFK.py.pdb
    no. of peptide chains: 27 [1=14,A=83,B=96,C=59,D=22,E=8,F=22,G=23,H=20,I=57,J=41,K=40,L=23,M=46,N=32,O=40,P=7,Q=25,R=7,S=8,T=25,U=15,V=37,W=14,X=27,Y=11
,Z=38]
    no. of DNA chains: 0 []
    no. of amino acids:    840
    no. of nucleotides:    2838
    no. of atoms:          61687
    no. of waters:         11
    no. of metals:         3 [Mg=2,K=1]
sws2@jabba:/media/HD/DATA/pdb_files_temp/1FFK$
*********

Thus, there are no contacts which seems strange.
(I attached the pdb file we used)

Also as you can see, the options we use are not recapitulated in the command line.
is that what you want ?

Best,

Pascal

16

DNA/RNA-protein interactions (SNAP) / Re: interaction code and other issues

« on: June 01, 2014, 04:54:31 pm »

Thanks Xiang-Jun,

For h_bonds in snap, can I use --hbond_d2=3.5 as in dssr ?

Best,

Pascal

17

DNA/RNA-protein interactions (SNAP) / interaction code and other issues

« on: June 01, 2014, 04:13:25 pm »

Hi Xiang-Jun,

Really great work, thanks.

Just a few remarks:
Why didn't you use the same nomenclature as in dssr ?
I mean using dots to separate the nucleotide name from its numbering.
For example in 4LT5, I see

****************************************************************************
List of 6 pair-wise phosphate-group/amino-acid H-bonding interactions
      id  nt-aa  nt           aa          H-bonds
   1 4LT5 G-lys B.DG9        A.LYS318     1:OP1-NZ[3.42]

B.DG9 could be B.DG.9
A.LYS318 could be A.LYS.318

Have you taken into account the segid code as you did for dssr ?

for the same structure, we defined a 3.5 cut-off
Command: x3dna-snap -i=/media/HD/DATA/pdb_files_temp/4LT5/4LT5.py.pdb -o=4LT5.py.snap.3.5.out --cutoff=3.5

yet we found
  2 4LT5 T-lys B.DT11       A.LYS303     1:OP1-NZ[3.71]  <---- greater than 3.5
   1 4LT5 T-lys B.DT10       A.LYS303     1:O3'-NZ[3.65]  <---- greater than 3.5

Thanks for looking at this,

Pascal

18

RNA structures (DSSR) / dssr corrupted double-linked list: issue

« on: January 31, 2014, 03:26:41 am »

Hi Xiang-Jun,

With the file 2OIU.py.pdb (see attached, I get the following message and dssr freeze:

*** glibc detected *** x3dna-dssr: corrupted double-linked list: 0x0000000001604530 ***

Thanks for help and best wishes for the Horse year.

Best,

Pascal

19

RNA structures (DSSR) / Re: dssr parameters

« on: October 17, 2013, 09:55:49 am »

OK, thanks, what about default values ?

Pascal

20

RNA structures (DSSR) / Re: dssr parameters

« on: October 17, 2013, 07:26:19 am »

Hi Xiang_Jun,

Thanks again for the help.
A last request would be to know what the default parameters are for these options (may be they could be
written down along with the current values when the "note" option is activated.

As for H-bonds, I used longer cut-offs for C-H...O bonds than for regular ones.
Usually for base pairs, I use the 3.35 and for C-H...O bonds, I add 0.5 Å to the preceding value.

Thus, a different cut-off for C-H...O bonds could be valuable at some point.
Similarly, a specific cut-off for other atoms like S could be interesting.

Best,

Pascal

21

RNA structures (DSSR) / Re: dssr parameters

« on: October 16, 2013, 03:23:55 pm »

Great Xiang-Jun,

Is there a possibility to set up different cut-offs for O/N...H and C-H...N bonds ?
That would be really awesome.

Best,

Pascal

22

RNA structures (DSSR) / Re: dssr parameters

« on: October 16, 2013, 12:14:43 pm »

Sorry,

forgot the "#   maximum angle between base normals (in range 0..90)"

Pascal

23

RNA structures (DSSR) / Re: dssr parameters

« on: October 16, 2013, 11:59:02 am »

Thanks Xiang-Jun,

In X3DNA, you had besides the ones you provided, the followings.

Parameters for defining bifurcated h-bonds,
The possibility to define atoms involved in h-bonding (O,N, or C)

The maximum vertical base separation (sorry for not having written the entire line down)
The maximum angle between base normals
The minimum distance between the RN/YN base atoms

Thanks for sharing more if you like,

Best,

Pascal

24

RNA structures (DSSR) / dssr parameters

« on: October 16, 2013, 10:47:08 am »

Hi Xiang-Jun,

The X3DNA package came with a configuration file named 'misc_3DNA.par'.
You showed me once how to precise the distance limit for hydrogen bonds in dssr.
What about the other parameters like those related to
the vertical base separation,
the maximum distance between base origin,
the maximum vertical separation,
...

Hope equivalent parameter sets are available in dssr.

Best regards,

Pascal

25

Feature requests / Notification on format changes

« on: September 18, 2013, 06:36:24 am »

Also as a slight suggestion, it would be nice for those who parse the 3DNA and dssr output to be notified when an update modifies the output format and eventually where.

Thanks again,

Pascal