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Topics - Auffinger

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1
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

2
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

3
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

4
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

5
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

6
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

7
DNA-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


8
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

9
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

10
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

11
RNA structures (DSSR) / dssr issue (for modified pdb files)
« on: September 03, 2013, 06:27:38 am »
Hi Xiang-Jun,

Just encountered following dssr (latest august release)

*** glibc detected *** x3dna-dssr: corrupted double-linked list: 0x000000000227cc50 ***

when using following file : 3CUL_REDO.py.pdb

this file is not an original pdb file, any idea where the error can come from ?
This file is not the only one but the occurrence of such errors is quite rare.

Thanks,

Pascal

12
RNA structures (DSSR) / A/B/Z forms
« on: August 03, 2013, 09:30:08 am »
Dear Xiang-Jun,

Thanks a lot for all the modifications you have done on request to your programs.
It is great that dssr provides now clues about the helix form for each base pair (and nucleotide).

Unfortunately, I think that the manner its added to the output files, although quite informative, is also
very difficult to parse. Could you imagine adding these A/B/Z labels to, for example, to
the torsion files (for dssr and also for 3DNA - this would be very useful to us
and hopefully to others too).

For example here for the dssr torsion file

        nt             bin    cluster   suiteness  A/B/Z/
 1     ..A.C.1.        inc      __       0.000      xxx
 2     ..A.DC.2.       33p      1a       0.824    xxx
 3     ..A.DG.3.       33p      1a       0.403    xxx
 4     ..A.DG.4.       33p      1a       0.387    xxx

and here for the 3DNA torsion file

              base      chi A/S     alpha    beta   gamma   delta  epsilon   zeta     e-z BI/BII     A/B/Z
   1 A:...1_:[..C]C  -161.7 anti     ---     ---     59.1    78.4  -155.0   -71.6   -83.4  BI         xxx
   2 A:...2_:[.DC]C  -163.8 anti    -60.6   156.1    55.3    82.7  -175.3   -64.1  -111.2  BI    xxx

Cheers,

Pascal

13
RNA structures (DSSR) / dealing with symmetrics
« on: June 17, 2013, 06:39:04 am »
Hi Xiang-Jun,

We are, besides regular interactions, also interested by interactions involving symmetric fragments.

As you perhaps know, pymol puts out PDB files with an additional four letter code (see below).
We are using this four letter code for expanding our evaluation of non-covalent interactions.

As such, could you eventually add an option to 3DNA and/or DSSR (like -sym) that would allow to differentiate original nucleotides from symmetric ones.

For example, see this PDB fragment generated by pymol from the 100D file.

HETATM  487  O   HOH B  77       1.829  -2.266   9.724  1.00 75.20           O 
HETATM  489  O   HOH B  79      -9.310  -1.446  19.391  1.00 71.79           O 
HETATM  411  N1  SPM A  21     -13.297  -8.783  22.839  1.00 40.13      AZ00 N 
HETATM  412  C2  SPM A  21     -12.449  -7.621  23.379  1.00 38.06      AZ00 C 
HETATM  413  C3  SPM A  21     -13.154  -6.312  23.033  1.00 36.69      AZ00 C 
HETATM  414  C4  SPM A  21     -12.226  -5.116  22.994  1.00 35.02      AZ00 C 

The four letter code is not something that is in the current PDB format but was allowed in previous versions.
In this example, it corresponds to a symmetry code that is specific to the used symmetry operations.

In DSSR, you could for example write:

  13 .A.DG.9.         .B.DC.12.*        G-C WC           19-XIX    cWW cW-W
Where the star indicates a symmetric.

You could also consider (better option)
  13 .A.DG.9.         .B.DC.12.1Z00        G-C WC           19-XIX    cWW cW-W
Where you would write the symmetric code in full.

This would be really greatly helpful to us.

Best,

Pascal




14
Bug reports / rotate_mol small bug
« on: June 07, 2013, 10:34:11 am »
Hi Xiang-Jun,

Just ran into a small issue with the new rotate_mol version.
I get a core dump with this file


ATOM     81  H01  DG A   4       0.252  -2.488  17.289  1.00  8.27           H 
ATOM     82  H02  DG A   4       3.942   1.573  19.159  1.00 11.82           H 
ATOM     70  N9   DG A   4       3.496   1.232  18.319  1.00 11.82           N 
ATOM     71  C8   DG A   4       3.617   1.742  17.054  1.00  8.09           C 
ATOM     72  N7   DG A   4       2.902   1.118  16.167  1.00 11.07           N 
ATOM     73  C5   DG A   4       2.252   0.091  16.894  1.00 11.16           C 
ATOM     74  C6   DG A   4       1.310  -0.920  16.456  1.00  9.75           C 
ATOM     76  N1   DG A   4       0.906  -1.749  17.502  1.00  8.27           N 
ATOM     77  C2   DG A   4       1.340  -1.630  18.818  1.00  8.31           C 
ATOM     79  N3   DG A   4       2.218  -0.681  19.223  1.00  9.10           N 
ATOM     80  C4   DG A   4       2.629   0.144  18.209  1.00 10.34           C 

Could you check ???

Thanks,

Pascal

15
RNA structures (DSSR) / C-H...O bonds
« on: June 06, 2013, 02:05:52 pm »
Hi Xiang-Jun,

Is there a way to define H-bond criteria for C-H...O bonds ?
Does DSSR calculate them ?
Any other hints about how to set up h-bonds in DSSR ?

Best,

Pascal

Pages: [1] 2

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.