Messages

26

RNA structures (DSSR) / Re: dealing with symmetrics

« on: September 18, 2013, 06:10:49 am »

Hi Xiang-Jun,

The --segid option works fine. Just encountered a new exception with attached file and option combination. (I send you the pdb file by mail since its too large).

29858 Segmentation fault      (core dumped) x3dna-dssr --non-pair --long-idstr --hbond_d2=3.5 --po4 --u-turn --segid -i=/media/HD/DATA/pdb_files_temp/3F1E/3F1E.py.pdb -o=3F1E.py.dssr.out

Thanks for having a look,

Best,

Pascal

27

RNA structures (DSSR) / Re: dealing with symmetrics

« on: September 16, 2013, 11:39:53 am »

Hi Xiang-Jun,

I like your new version. Unfortunately, I think that I lost the
ability to include the PDB segID into the dssr out files
as you implemented it recently!

  28 .B000.B.G.20.    .CA00.B.DC.15.   G-C              00-n/a    cSS tm-m
       -147.2(anti) C3'-endo lambda=109.9; -152.0(anti) C2'-exo lambda=109.8
       d(C1'-C1')=5.30 d(N1-N9)=6.63 d(C6-C8)=8.75 tor(N1-C1'-C1'-N9)=95.6
       H-bonds[1]: "N2(amino)-O2(carbonyl)[3.10]"

I join two files in order for you to check if may be the pdb
file we used causes the problem.

Best,

Pascal

28

RNA structures (DSSR) / Re: dssr issue (for modified pdb files)

« on: September 04, 2013, 09:16:51 am »

Thanks, works fine for this file.

Best,

Pascal

29

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

30

RNA structures (DSSR) / Re: A/B/Z forms

« on: August 05, 2013, 08:54:29 am »

Hi Xiang-Jun,

I understand your concerns. For me it is more related to having this
info somewhere in your dssr output files for easy parsing where ever the
right place might be.

As it is it's just very difficult to parse.

You say that the algorithm used is different from that in 3DNA.
Could you comment on that ?

Thanks,

Pascal

31

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

32

RNA structures (DSSR) / Re: dealing with symmetrics

« on: June 17, 2013, 10:54:49 am »

Ok, but I don't see it working on my screen. I tried !
I join a pdb file that contains segid and that was generated by pymol.
Any timeline for a new version ?

Pascal

33

RNA structures (DSSR) / Re: dealing with symmetrics

« on: June 17, 2013, 10:20:05 am »

Xiang-Jun,

Thats good news.
Basically, pymol uses the segment identifier code defined here:

http://deposit.rcsb.org/adit/docs/pdb_atom_format.html

at the "Record: ATOM" line:
73 - 76        LString(4)      Segment identifier, left-justified.

See this example (A1  )
       
ATOM    145  N   VAL A  25      32.433  16.336  57.540  1.00 11.92      A1   N

or (AZ00)

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

(sorry for the fact that I am unable to write these lines with an non-proportional font)

pymol uses these specifications.

Yet, this is an old pdb definition as you can judge from the most recent one
http://www.wwpdb.org/documentation/format33/sect9.html#ATOM
that does not mention a segment identifier.

Here is what I found in pymol documentation
---
“segment” selects atoms based on their assigned chain, which is a four-letter code.

A PyMOL Segment is a set of atoms within a single molecular object that share all property identifiers except atom names, residue and chain property identifiers.

Segments are most useful in cases where multiple copies of an identical set of chains must exist inside of a single molecular object. They also come in handy for complex proteins which have more chains than can represented with a single-character alphanumeric identifier.
---
Would be great if you could make this work,
Thanks for considering it,

Pascal

34

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

35

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

36

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

37

RNA structures (DSSR) / Re: list nucleotide/nucleotide contacts involving a phosphate group.

« on: May 07, 2013, 01:40:06 pm »

Hi Xiang-Jun,

Thanks again for the quick reply. I understand your point of view.
It is not about putting things aside, just ordering them differently.
I am sure that some other things will have to be detected in RNA structures
and for that we really need the maximum of info and your software is a great tool for this.

In the present case its more a philosophical point and I suppose that some
people out there will run into the same interrogations as us.

Thus, providing another output type seems a great option and I suggest
a roughly identical file format where in the first section only base base interactions are listed
and where base-backbone and backbone-backbone interactions appear in the "non-pairing interaction" list
which could be labeled more appropriately "Base-base and base-backbone interactions".

Thanks for proposing to work on this and thanks for the work you have already done.

Pascal

38

RNA structures (DSSR) / Re: list nucleotide/nucleotide contacts involving a phosphate group.

« on: May 07, 2013, 11:21:20 am »

Dear Xiang-Jun,

To follow this line of question, it seems to us that some information are not found at their expected (for us) location.
For example, if we take the 2Z75 structure from the PDB:

We find this base-pairing info for residue 114 chain B

  68 B.G114           B.A117           [G-A]              00-n/a    tSH tm-M
       -162.1(anti) C3'-endo lambda=85.5; -127.3(anti) C3'-endo lambda=20.6
       d(C1'-C1')=10.02 d(N1-N9)=8.75 d(C6-C8)=8.73 tor(N1-C1'-C1'-N9)=-147.9
       H-bonds[3]: "N1(imino)-OP2[2.96]; N2(amino)-OP2[2.56]; N2(amino)-N7[3.08]"

These lines do not only list base-base interactions, but also base-phosphate-interactions (in other instances also base-sugar information).
I believe that here we should only find base-base interactions
and that base backbone information should be placed in the "non-pairing interaction" list.

Furthermore, the H-bond count of 3 seems not appropriate for the base-base interaction.
may be, you could write

       H-bonds[1]: "N2(amino)-N7[3.08]" followed by
       H-bonds_backbone[2]: "N1(imino)-OP2[2.96]; N2(amino)-OP2[2.56]"

and also list this last line in the "non-pairing interaction" list since you already have lines like
   5 A.G1             B.G39           base-overlap-area=0.0(0.0)
       H-bonds[2]: "OP1-N1(imino)[2.73]; OP1-N2(amino)[3.39]"

Hope you agree to that,

Best Pascal

39

General discussions (Q&As) / Re: possible rotate_mol labeling issue

« on: April 30, 2013, 12:19:50 pm »

Hi Xiang-Jun,

Sorry for not having replied earlier. I thing you can use any file containing a nucleotide and if you use the file -pdbv3=false, the program turns OP1/2 into O1/2P.
If you take any base file as the one I sent you earlier (see above) then the residue labels might get changed C->DC, G->DG, and so on, The only way to solve this is the -pdbv3=false option, thus this option is good for base files but not for nucleotides, basically.

That describes the problem, I think.

Pascal

40

General discussions (Q&As) / Re: possible rotate_mol labeling issue

« on: April 26, 2013, 02:06:27 pm »

Hi Xiang-Jun,

Sorry to continue with this issue but I realized that with the pdbv3=false option, I get the old O1P/O2P back which certainly something I don't want.
I must say I am stuck here. In one case wrong phosphate names in the other wrong residue names.

When I wrote rely on the pdb file, I meant that for the residue names. Why check if they are correct and eventually bother to change them ?
It seems to me an unnecessary task.

Please, I would appreciate your quick help on this.
In the mean time I used a sed command.

Best,

Pascal

41

RNA structures (DSSR) / Re: list nucleotide/nucleotide contacts involving a phosphate group.

« on: April 25, 2013, 06:49:19 am »

Hi Xiang-Jun,

I understand your point of view, yet if its not explained it looks a little bit weird.
thus, I think that writing a maximum of explanations in the files themselves would really be useful.

My point of view is that if you shift the pucker by one space, no one will really understand why unless explained.
Even though, it might be difficult for people trying to parse the files by using a strict format.

Same for the ~. Believe me, I can spend a lot of time wondering why this is and come up sometimes
but not always with a correct answer.

So best, is not having to guess or to wonder.

Do you agree ?

Pascal

42

RNA structures (DSSR) / Re: list nucleotide/nucleotide contacts involving a phosphate group.

« on: April 24, 2013, 12:41:54 pm »

Hi Xiang-Jun,

Just found your explanation about the pucker values at the top of the torsions file :

  phase-angle: the phase angle of pseudorotation and puckering
  sugar-type: sugar classification into C3'-like or C2'-like

Think its great to have such comments in the data files, it helps a lot to understand and refresh memory.
One case where redundancy is useful.

Yet, I noted a misalignment at some places with the ~C2'-endo value.

 6     A.A2654           165.2   133.8    56.7   149.4   -98.3   161.4    100(BII)  -145.3(anti)   151.0(C2'-endo) ~C2'-endo     0.91    0.92
 7     A.G2655           -96.2    91.7   179.3   149.3  -167.2   141.4     51        -93.5(anti)   151.5(C2'-endo) ~C2'-endo     2.15    2.14
 8     A.U2656           -72.5   157.8    37.9    91.6  -141.0   -65.6    -75(BI)   -173.9(anti)     0.4(C3'-endo)  ~C3'-endo    4.35    4.42
 9     A.A2657           -68.7   174.5    50.2    83.7  -145.1   -61.1    -84(BI)   -171.1(anti)    26.5(C3'-endo)  ~C3'-endo    4.49    4.52

also, whats the reason for the "~" ?

Pascal

43

RNA structures (DSSR) / Re: list nucleotide/nucleotide contacts involving a phosphate group.

« on: April 24, 2013, 10:26:34 am »

Hi Xiang-Jun,

Thats just great. It looks like a combined version of find_pair and analyze. Is that correct ?
Of course it seems not possible to (re)construct NA structures with DSSR.

So first, why calling it DSSR and not DSSNA since it works also for DNA ?
I think that one should avoid the RNA domination, it is possible to learn from both structures.
thus, does DSSR really work for DNA ?

____

Then, as for formats,
I think that as I mentioned it somewhere earlier, and since I am processing the output files
for a large number of structures, I appreciate when there are spacesbetween fields (see).

For exemple, in the dssr-torsion.dat file :
 
      base_id            alpha    beta   gamma   delta  epsilon   zeta     e-z        chi            phase-angle   sugar-type     Zp      Dp
 1     A.C2649            ---    167.1    47.6    84.1  -146.6   -77.1    -69(BI)   -160.5(anti)    12.9(C3'-endo)  ~C3'-endo    4.41    4.66
 2     A.U2650           -64.2   164.2    60.3    79.8  -154.5   -73.1    -81(BI)   -167.2(anti)    21.3(C3'-endo)  ~C3'-endo    4.40    4.55

is easier to process if you write:
 2     A.U2650           -64.2   164.2    60.3    79.8  -154.5   -73.1    -81 (BI)   -167.2 (anti)    21.3 (C3'-endo)  ~C3'-endo    4.40    4.55

and is there a need for writing twice the sugar pucker in this file ?

---
you name this file torsion although there are sugar puckers in it.
Thus it might be called torsion_puckers.dat or something else.

---
For the non-pairing interactions that is just a great feature,

you had before two values for base overlap
one calculated by just using ring atoms the other by using all base atoms.

you could add this.

---

Why adding the name of the chemical groups (hydroxyl, amino, imino, ...)
again this complicates reading since some groups are named and others not like OP2 and so on.

I would appreciate another presentation here.

___

I haven't really checked, but are your base pair numbering scheme coherent with the one
you use in find_pair ? It would be really nice to be the case.

___

Also, I wanted to ask you that but know it seems to be done. You add various names
to each base pair. Thats great. Just a hint to the various nomenclatures (Leontis-Westhof, Saenger...)
would be helpful in the *.out files.

---

is there a configuration file that would allow to precise hydrogen bond and other parameters like in 3DNA.
I would really appreciate that.

---

more later,

Tanks for the great work,

Pascal

44

General discussions (Q&As) / Re: possible rotate_mol labeling issue

« on: April 23, 2013, 11:48:56 am »

Hi Xiang-Jun,

Yes, but what would you do for terminal residues that lack phosphate groups. Why not simply rely on the pdb author labeling ?
As for manuals, I understand your point. One way to solve this would be to include a manual for all options
available through a -help option. This manual would be updated along with the addition/modification of program options.
And all users could rely on this.


Pascal

45

General discussions (Q&As) / Re: possible rotate_mol labeling issue

« on: April 23, 2013, 04:33:20 am »

Hi Xiang-Jun,

I tried to be careful by not saying that this was a bug since I know that you are very thoughtful about your programs and was thinking that this was related to unknown options/features of your program.
First, it would be nice to have manuals for them but I know you are working on them.
Then, you should may be have a forum topic for clarification issues (the bug report was my only possible choice - sorry).

For now, I tried the -pdbv3 option and it solves my issue, thanks.

On the other side, I think that you may be should reconsider the option of checking if an O2' is present since it lacks universality.
I was living with this program behavior for a while without realizing that I didn't get the expected results.
Just pay attention to your definition of backbone atoms.
Some files might contain C1' atoms and no other backbone atoms, so this seems a tricky issue.

Best,

Pascal

46

General discussions (Q&As) / possible rotate_mol labeling issue

« on: April 22, 2013, 02:53:17 pm »

Dear Xiang-Jun,

I noticed an odd behavior of rotate_mol

If I apply the command
rotate_mol -ac to the coordinates below I get an output where the residue C is changed for a DC

original file

ATOM    814  C1'   C A  38       3.595   3.773  -0.589  1.00 73.86           C 
ATOM    815  N1    C A  38       4.587   2.642  -0.702  1.00 73.00           N 
ATOM    816  C2    C A  38       5.926   2.894  -1.060  1.00 73.87           C 
ATOM    817  O2    C A  38       6.307   4.051  -1.290  1.00 74.90           O 
ATOM    818  N3    C A  38       6.791   1.846  -1.144  1.00 73.76           N 
ATOM    819  C4    C A  38       6.371   0.600  -0.888  1.00 72.72           C 
ATOM    820  N4    C A  38       7.261  -0.396  -0.986  1.00 72.70           N 
ATOM    821  C5    C A  38       5.018   0.320  -0.526  1.00 71.49           C 
ATOM    822  C6    C A  38       4.176   1.359  -0.445  1.00 71.64           C 

output

REMARK    3DNA v2.1 (c) 2013 Dr. Xiang-Jun Lu (xiangjun@x3dna.org; http://x3dna.org)
ATOM      1  C1'  DC A  38      -0.773  -2.615  -0.004  1.00 73.86           C 
ATOM      2  N1   DC A  38      -0.478  -1.136   0.003  1.00 73.00           N 
ATOM      3  C2   DC A  38       0.851  -0.668   0.002  1.00 73.87           C 
ATOM      4  O2   DC A  38       1.797  -1.468  -0.001  1.00 74.90           O 
ATOM      5  N3   DC A  38       1.074   0.675   0.001  1.00 73.76           N 
ATOM      6  C4   DC A  38       0.044   1.532  -0.002  1.00 72.72           C 
ATOM      7  N4   DC A  38       0.317   2.843  -0.002  1.00 72.70           N 
ATOM      8  C5   DC A  38      -1.312   1.081   0.001  1.00 71.49           C 
ATOM      9  C6   DC A  38      -1.519  -0.243   0.001  1.00 71.64           C 
END

This is kid of odd and happens for all the files of that kind.

Can you check this ?
I used the latest download.

Best,

Pascal

47

RNA structures (DSSR) / Re: list nucleotide/nucleotide contacts involving a phosphate group.

« on: April 05, 2013, 11:35:46 am »

Hi Xiang-Jun,

Thanks for this quick reply.
I would be happy to try this out first for the non-base-base contacts.
Then of course stacking info would be great.

I suggest to add a stacking output file that would list stacking info in the usual way.
You will certainly find a good way to do that. I guess you would add info related to
the stacking of non-connected nucleotides. I am eager to see that.

Thanxs,

Pascal

48

RNA structures (DSSR) / list nucleotide/nucleotide contacts involving a phosphate group.

« on: April 05, 2013, 10:38:46 am »

Hi Xiang-Jun,

I was wondering if 3DNA provides (with some unknown options to me) a listing of the nucleotides that are linked by hydrogen bonds other than base-base ones.
For example, if two nucleotides interact by a single base/phosphate or a base/sugar or supar/phosphate contact, is there a way to get a list of them.
(of course this might involve specific hydrogen bond parameters).
Hope this is clear.

Best,

Pascal

49

Feature requests / Re: chain continuation character in analyze

« on: August 09, 2012, 10:36:59 am »

Hi Xiang-Jun,

Thanks, works quite fine and its nice to have '+' for isolated nucleotides on top of it.
Hope it will be useful to others than me,

Best,

Pascal

50

Feature requests / Re: chain continuation character in analyze

« on: August 08, 2012, 11:52:50 am »

Well if its a lot of work, I understand.
for me, since I treat automatically, all pdb files, I thought it would be simple to change it for  analyze with the -s option (thought it is basically the same as with no option).
It would facilitate my work, but I can (will have to may be) use  workarounds.
Let me know if you can do it.

Is the option -pdbv3 standard also for O1P_O2P ?

Best,

Pascal