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Questions and answers => RNA structures (DSSR) => Topic started by: auffinger on June 17, 2013, 06:39:04 am

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Title: dealing with symmetrics
Post by: auffinger 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

Title: Re: dealing with symmetrics
Post by: xiangjun on June 17, 2013, 09:01:57 am

Could you provide (a link to) the full specification of the PyMOL-customerized PDB format with a complete example? I may consider to handle the extra symmetric fragment if the functionality fits the overall design of DSSR.

Xiang-Jun

Title: Re: dealing with symmetrics
Post by: auffinger 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

Title: Re: dealing with symmetrics
Post by: xiangjun on June 17, 2013, 10:36:15 am

Okay, I got the idea, and I will take segid into consideration in the next release of DSSR.

To use fixed space font, you could try Tt button, # button for code, or pre-formatted text button -- all on the menu, in a similar fashion as in Word.

Xiang-Jun

Title: Re: dealing with symmetrics
Post by: auffinger 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

Title: Re: dealing with symmetrics
Post by: xiangjun on June 17, 2013, 11:07:11 am

Quote

Ok, but I don't see it working on my screen. I tried !

Weird. Then your settings are not the default. You can type the formatting BBcode (http://en.wikipedia.org/wiki/BBCode) manually, as below:

[tt]...[/tt]
[code]...[/code]
[pre]...[/pre]

Quote

I join a pdb file that contains segid and that was generated by pymol.

Thanks for sample PDB file with segid.

Quote

Any timeline for a new version ?

It won't be long, hopefully. In the meantime, could you reply to my posts that address your previous requests?

Xiang-Jun

Title: Re: dealing with symmetrics
Post by: xiangjun on June 18, 2013, 06:20:57 pm

Hi Pascal,

I've updated DSSR to beta-r13-on-20130618 which took into consideration of segid, among other refinements. Using your sample PDB file as an example, the output is as below:

Code: [Select]

 Run: x3dna-dssr -i=100d.py.pdb -o=100d.py.out --long-idstr  --note=no

****************************************************************************
    DSSR: Software for Defining the (Secondary) Structures of RNA
      by Xiang-Jun Lu (xiangjun@x3dna.org), beta-r13-on-20130618

   The program is currently under active development. As always, we
   greatly appreciate your feedback! Please report all DSSR-related
   issues on the 3DNA Forum (http://forum.x3dna.org/). I strive to
   respond promptly to any questions posted there.

****************************************************************************
Date and time: Tue Jun 18 22:23:15 2013
File name: 100d.py.pdb
    no. of DNA/RNA chains: 2 [A=24, B=25]
    no. of nucleotides:    49
    no. of waters:         92
    no. of metals:         0

****************************************************************************
List of 35 base pair(s)
   1 ..A.C.1.         ..B.G.20.        C-G WC           19-XIX    cWW cW-W
       -161.7(anti) C3'-endo lambda=54.3; -147.2(anti) C3'-endo lambda=54.3
       d(C1'-C1')=10.74 d(N1-N9)=9.02 d(C6-C8)=9.92 tor(N1-C1'-C1'-N9)=-17.1
       H-bonds[3]: "O2(carbonyl)-N2(amino)[2.77]; N3-N1(imino)[2.93]; N4(amino)-O6(carbonyl)[2.93]"
       bp_pars: [0.07    -0.09   0.04    3.92    -8.78   -0.90]
   2 ..A.DC.2.        ..B.DG.19.       C-G WC           19-XIX    cWW cW-W
       -163.8(anti) C3'-endo lambda=52.9; -173.5(anti) C3'-endo lambda=52.9
       d(C1'-C1')=10.70 d(N1-N9)=8.93 d(C6-C8)=9.82 tor(N1-C1'-C1'-N9)=-13.1
       H-bonds[3]: "O2(carbonyl)-N2(amino)[2.72]; N3-N1(imino)[2.87]; N4(amino)-O6(carbonyl)[2.83]"
       bp_pars: [-0.02   -0.17   -0.06   4.83    -9.56   -1.89]
   3 ..A.DG.3.        ..B.DC.18.       G-C WC           19-XIX    cWW cW-W
       -156.0(anti) C3'-endo lambda=55.2; -163.4(anti) C3'-endo lambda=54.8
       d(C1'-C1')=10.58 d(N1-N9)=8.90 d(C6-C8)=9.85 tor(N1-C1'-C1'-N9)=-17.6
       H-bonds[3]: "O6(carbonyl)-N4(amino)[3.08]; N1(imino)-N3[2.91]; N2(amino)-O2(carbonyl)[2.68]"
       bp_pars: [-0.35   -0.16   -0.04   2.66    -10.59  1.38]
   4 ..A.DG.3.        .B00A.A.G.10.    G-G              00-n/a    c.S c.-m
       -156.0(anti) C3'-endo lambda=108.7; -153.1(anti) C3'-endo lambda=149.2
       d(C1'-C1')=5.60 d(N1-N9)=7.39 d(C6-C8)=9.83 tor(N1-C1'-C1'-N9)=-26.9
       H-bonds[2]: "N2(amino)-N3[3.23]; N3-O2'(hydroxyl)[2.69]"
       bp_pars: [-2.57   7.21    -2.45   -44.65  21.25   152.60]
   5 ..A.DG.4.        ..B.DC.17.       G-C WC           19-XIX    cWW cW-W
       -143.6(anti) C3'-endo lambda=53.5; -161.7(anti) C3'-endo lambda=53.8
       d(C1'-C1')=10.66 d(N1-N9)=8.91 d(C6-C8)=9.84 tor(N1-C1'-C1'-N9)=-23.0
       H-bonds[3]: "O6(carbonyl)-N4(amino)[2.88]; N1(imino)-N3[2.80]; N2(amino)-O2(carbonyl)[2.67]"
       bp_pars: [-0.24   -0.20   0.09    -2.07   -10.90  0.44]
   6 ..A.DG.4.        .B00A.A.G.10.    G-G              00-n/a    cSS tm-m
       -143.6(anti) C3'-endo lambda=110.1; -153.1(anti) C3'-endo lambda=103.0
       d(C1'-C1')=4.65 d(N1-N9)=5.97 d(C6-C8)=7.86 tor(N1-C1'-C1'-N9)=109.9
       H-bonds[1]: "N3-N2(amino)[3.15]"
       bp_pars: [-2.15   -7.43   1.59    46.36   -29.54  -165.95]
   7 ..A.DG.4.        .B00A.B.C.11.    G+C              00-n/a    tS. tm+.
       -143.6(anti) C3'-endo lambda=82.8; -159.1(anti) C3'-endo lambda=73.0
       d(C1'-C1')=9.02 d(N1-N9)=8.85 d(C6-C8)=11.20 tor(N1-C1'-C1'-N9)=-147.3
       H-bonds[1]: "N2(amino)-O2(carbonyl)[3.36]"
       bp_pars: [-2.30   -7.57   2.20    41.36   -27.41  -161.33]
   8 ..A.DC.5.        ..B.DG.16.       C-G WC           19-XIX    cWW cW-W
       -163.6(anti) C3'-endo lambda=57.0; -164.3(anti) C3'-endo lambda=55.2
       d(C1'-C1')=10.41 d(N1-N9)=8.78 d(C6-C8)=9.71 tor(N1-C1'-C1'-N9)=-15.6
       H-bonds[3]: "O2(carbonyl)-N2(amino)[2.73]; N3-N1(imino)[2.81]; N4(amino)-O6(carbonyl)[2.84]"
       bp_pars: [0.38    -0.31   0.40    3.58    -12.55  -0.99]
   9 ..A.DG.6.        ..B.DC.15.       G-C WC           19-XIX    cWW cW-W
       -158.8(anti) C3'-endo lambda=54.6; -152.0(anti) C2'-exo lambda=55.3
       d(C1'-C1')=10.85 d(N1-N9)=9.16 d(C6-C8)=10.10 tor(N1-C1'-C1'-N9)=-24.1
       H-bonds[3]: "O6(carbonyl)-N4(amino)[3.02]; N1(imino)-N3[3.07]; N2(amino)-O2(carbonyl)[2.91]"
       bp_pars: [-0.16   0.05    0.03    -1.64   -16.84  0.00]
  10 ..A.DC.7.        ..B.DG.14.       C-G WC           19-XIX    cWW cW-W
       -153.4(anti) C3'-endo lambda=56.2; -162.2(anti) C3'-endo lambda=54.8
       d(C1'-C1')=10.52 d(N1-N9)=8.85 d(C6-C8)=9.78 tor(N1-C1'-C1'-N9)=-15.6
       H-bonds[3]: "O2(carbonyl)-N2(amino)[2.67]; N3-N1(imino)[2.81]; N4(amino)-O6(carbonyl)[2.85]"
       bp_pars: [0.42    -0.26   -0.10   2.69    -7.28   0.66]
  11 ..A.DC.7.        .D000.B.G.20.    C+G              00-n/a    tSW tm+W
       -153.4(anti) C3'-endo lambda=86.2; -147.2(anti) C3'-endo lambda=51.8
       d(C1'-C1')=8.36 d(N1-N9)=7.77 d(C6-C8)=9.62 tor(N1-C1'-C1'-N9)=145.0
       H-bonds[1]: "O2(carbonyl)-N2(amino)[2.92]"
       bp_pars: [-2.42   -7.23   2.20    -58.75  -25.30  -144.63]
  12 ..A.DC.8.        ..B.DG.13.       C-G WC           19-XIX    cWW cW-W
       -170.0(anti) C3'-endo lambda=57.0; -178.7(anti) C2'-exo lambda=52.7
       d(C1'-C1')=10.66 d(N1-N9)=8.96 d(C6-C8)=9.90 tor(N1-C1'-C1'-N9)=-5.4
       H-bonds[3]: "O2(carbonyl)-N2(amino)[2.74]; N3-N1(imino)[2.96]; N4(amino)-O6(carbonyl)[3.06]"
       bp_pars: [0.53    -0.13   -0.14   2.56    -6.75   2.31]
  13 ..A.DG.9.        ..B.DC.12.       G-C WC           19-XIX    cWW cW-W
       -172.0(anti) C3'-endo lambda=50.1; -151.8(anti) C3'-endo lambda=55.4
       d(C1'-C1')=10.78 d(N1-N9)=8.97 d(C6-C8)=9.86 tor(N1-C1'-C1'-N9)=-7.2
       H-bonds[3]: "O6(carbonyl)-N4(amino)[2.88]; N1(imino)-N3[2.85]; N2(amino)-O2(carbonyl)[2.69]"
       bp_pars: [-0.09   -0.14   -0.09   -3.82   -2.75   0.30]
  14 ..A.G.10.        ..B.C.11.        G-C WC           19-XIX    cWW cW-W
       -153.1(anti) C3'-endo lambda=51.2; -159.1(anti) C3'-endo lambda=53.6
       d(C1'-C1')=10.60 d(N1-N9)=8.79 d(C6-C8)=9.60 tor(N1-C1'-C1'-N9)=-14.5
       H-bonds[3]: "O6(carbonyl)-N4(amino)[2.63]; N1(imino)-N3[2.67]; N2(amino)-O2(carbonyl)[2.64]"
       bp_pars: [-0.26   -0.41   -0.03   -0.15   -5.96   -3.32]
  15 ..A.G.10.        .B000.A.DG.3.    G-G              00-n/a    cS. cm-.
       -153.1(anti) C3'-endo lambda=149.2; -156.0(anti) C3'-endo lambda=108.7
       d(C1'-C1')=5.60 d(N1-N9)=7.39 d(C6-C8)=9.83 tor(N1-C1'-C1'-N9)=-26.9
       H-bonds[2]: "O2'(hydroxyl)-N3[2.69]; N3-N2(amino)[3.23]"
       bp_pars: [2.57    7.21    -2.45   44.65   21.25   152.60]
  16 ..A.G.10.        .B000.A.DG.4.    G-G              00-n/a    cSS tm-m
       -153.1(anti) C3'-endo lambda=103.0; -143.6(anti) C3'-endo lambda=110.1
       d(C1'-C1')=4.65 d(N1-N9)=5.97 d(C6-C8)=7.86 tor(N1-C1'-C1'-N9)=109.9
       H-bonds[1]: "N2(amino)-N3[3.15]"
       bp_pars: [2.15    -7.43   1.59    -46.36  -29.54  -165.95]
  17 ..A.G.10.        .B000.B.DC.18.   G+C              00-n/a    tWS tW+m
       -153.1(anti) C3'-endo lambda=58.2; -163.4(anti) C3'-endo lambda=85.5
       d(C1'-C1')=8.53 d(N1-N9)=8.08 d(C6-C8)=10.10 tor(N1-C1'-C1'-N9)=150.3
       H-bonds[1]: "N2(amino)-O2(carbonyl)[3.02]"
       bp_pars: [2.68    7.77    -1.82   55.69   20.84   153.44]
  18 ..B.C.11.        .B000.A.DG.4.    C+G              00-n/a    t.S t.+m
       -159.1(anti) C3'-endo lambda=73.0; -143.6(anti) C3'-endo lambda=82.8
       d(C1'-C1')=9.02 d(N1-N9)=8.85 d(C6-C8)=11.20 tor(N1-C1'-C1'-N9)=-147.3
       H-bonds[1]: "O2(carbonyl)-N2(amino)[3.36]"
       bp_pars: [2.30    7.57    -2.20   -41.36  27.41   161.33]
  19 ..B.DG.14.       .D000.B.G.20.    G-G              00-n/a    cWS cW-m
       -162.2(anti) C3'-endo lambda=106.8; -147.2(anti) C3'-endo lambda=144.4
       d(C1'-C1')=5.59 d(N1-N9)=7.23 d(C6-C8)=9.62 tor(N1-C1'-C1'-N9)=-16.3
       H-bonds[2]: "N2(amino)-N3[2.91]; N3-O2'(hydroxyl)[2.76]"
       bp_pars: [-2.32   6.66    -2.35   -52.39  21.07   146.45]
  20 ..B.DC.15.       .D000.B.G.20.    C-G              00-n/a    cSS tm-m
       -152.0(anti) C2'-exo lambda=109.8; -147.2(anti) C3'-endo lambda=109.9
       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]: "O2(carbonyl)-N2(amino)[3.10]"
       bp_pars: [1.68    7.67    0.61    -44.53  37.97   179.58]
  21 ..B.DC.18.       .B00A.A.G.10.    C+G              00-n/a    tSW tm+W
       -163.4(anti) C3'-endo lambda=85.5; -153.1(anti) C3'-endo lambda=58.2
       d(C1'-C1')=8.53 d(N1-N9)=8.08 d(C6-C8)=10.10 tor(N1-C1'-C1'-N9)=150.3
       H-bonds[1]: "O2(carbonyl)-N2(amino)[3.02]"
       bp_pars: [-2.68   -7.77   1.82    -55.69  -20.84  -153.44]
  22 ..B.G.20.        .D0A0.A.DC.7.    G+C              00-n/a    tWS tW+m
       -147.2(anti) C3'-endo lambda=51.8; -153.4(anti) C3'-endo lambda=86.2
       d(C1'-C1')=8.36 d(N1-N9)=7.77 d(C6-C8)=9.62 tor(N1-C1'-C1'-N9)=145.0
       H-bonds[1]: "N2(amino)-O2(carbonyl)[2.92]"
       bp_pars: [2.42    7.23    -2.20   58.75   25.30   144.63]
  23 ..B.G.20.        .D0A0.B.DG.14.   G-G              00-n/a    cSW cm-W
       -147.2(anti) C3'-endo lambda=144.4; -162.2(anti) C3'-endo lambda=106.8
       d(C1'-C1')=5.59 d(N1-N9)=7.23 d(C6-C8)=9.62 tor(N1-C1'-C1'-N9)=-16.3
       H-bonds[2]: "O2'(hydroxyl)-N3[2.76]; N3-N2(amino)[2.91]"
       bp_pars: [2.32    6.66    -2.35   52.39   21.07   146.45]
  24 ..B.G.20.        .D0A0.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]"
       bp_pars: [-1.68   7.67    0.61    44.53   37.97   179.58]
  25 .B000.A.DG.3.    .B000.B.DC.18.   G-C WC           19-XIX    cWW cW-W
       -156.0(anti) C3'-endo lambda=55.2; -163.4(anti) C3'-endo lambda=54.8
       d(C1'-C1')=10.58 d(N1-N9)=8.90 d(C6-C8)=9.85 tor(N1-C1'-C1'-N9)=-17.6
       H-bonds[3]: "O6(carbonyl)-N4(amino)[3.08]; N1(imino)-N3[2.91]; N2(amino)-O2(carbonyl)[2.68]"
       bp_pars: [-0.35   -0.16   -0.04   2.66    -10.59  1.38]
  26 .B000.A.DG.4.    .B000.B.DC.17.   G-C WC           19-XIX    cWW cW-W
       -143.6(anti) C3'-endo lambda=53.5; -161.7(anti) C3'-endo lambda=53.8
       d(C1'-C1')=10.66 d(N1-N9)=8.91 d(C6-C8)=9.84 tor(N1-C1'-C1'-N9)=-23.0
       H-bonds[3]: "O6(carbonyl)-N4(amino)[2.88]; N1(imino)-N3[2.80]; N2(amino)-O2(carbonyl)[2.67]"
       bp_pars: [-0.24   -0.20   0.09    -2.07   -10.90  0.44]
  27 .B000.B.G.20.    .CA00.B.DG.14.   G-G              00-n/a    cSW cm-W
       -147.2(anti) C3'-endo lambda=144.4; -162.2(anti) C3'-endo lambda=106.8
       d(C1'-C1')=5.59 d(N1-N9)=7.23 d(C6-C8)=9.62 tor(N1-C1'-C1'-N9)=-16.3
       H-bonds[2]: "O2'(hydroxyl)-N3[2.76]; N3-N2(amino)[2.91]"
       bp_pars: [2.32    6.66    -2.35   52.39   21.07   146.45]
  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]"
       bp_pars: [-1.68   7.67    0.61    44.53   37.97   179.58]
  29 .C000.A.G.10.    .D000.A.DG.3.    G-G              00-n/a    cS. cm-.
       -153.1(anti) C3'-endo lambda=149.2; -156.0(anti) C3'-endo lambda=108.7
       d(C1'-C1')=5.60 d(N1-N9)=7.39 d(C6-C8)=9.83 tor(N1-C1'-C1'-N9)=-26.9
       H-bonds[2]: "O2'(hydroxyl)-N3[2.69]; N3-N2(amino)[3.23]"
       bp_pars: [2.57    7.21    -2.45   44.65   21.25   152.60]
  30 .D000.A.C.1.     .D000.B.G.20.    C-G WC           19-XIX    cWW cW-W
       -161.7(anti) C3'-endo lambda=54.3; -147.2(anti) C3'-endo lambda=54.3
       d(C1'-C1')=10.74 d(N1-N9)=9.02 d(C6-C8)=9.92 tor(N1-C1'-C1'-N9)=-17.1
       H-bonds[3]: "O2(carbonyl)-N2(amino)[2.77]; N3-N1(imino)[2.93]; N4(amino)-O6(carbonyl)[2.93]"
       bp_pars: [0.07    -0.09   0.04    3.92    -8.78   -0.90]
  31 .B00A.A.DG.9.    .B00A.B.DC.12.   G-C WC           19-XIX    cWW cW-W
       -172.0(anti) C3'-endo lambda=50.1; -151.8(anti) C3'-endo lambda=55.4
       d(C1'-C1')=10.78 d(N1-N9)=8.97 d(C6-C8)=9.86 tor(N1-C1'-C1'-N9)=-7.2
       H-bonds[3]: "O6(carbonyl)-N4(amino)[2.88]; N1(imino)-N3[2.85]; N2(amino)-O2(carbonyl)[2.69]"
       bp_pars: [-0.09   -0.14   -0.09   -3.82   -2.75   0.30]
  32 .B00A.A.G.10.    .B00A.B.C.11.    G-C WC           19-XIX    cWW cW-W
       -153.1(anti) C3'-endo lambda=51.2; -159.1(anti) C3'-endo lambda=53.6
       d(C1'-C1')=10.60 d(N1-N9)=8.79 d(C6-C8)=9.60 tor(N1-C1'-C1'-N9)=-14.5
       H-bonds[3]: "O6(carbonyl)-N4(amino)[2.63]; N1(imino)-N3[2.67]; N2(amino)-O2(carbonyl)[2.64]"
       bp_pars: [-0.26   -0.41   -0.03   -0.15   -5.96   -3.32]
  33 .D0A0.A.DG.6.    .D0A0.B.DC.15.   G-C WC           19-XIX    cWW cW-W
       -158.8(anti) C3'-endo lambda=54.6; -152.0(anti) C2'-exo lambda=55.3
       d(C1'-C1')=10.85 d(N1-N9)=9.16 d(C6-C8)=10.10 tor(N1-C1'-C1'-N9)=-24.1
       H-bonds[3]: "O6(carbonyl)-N4(amino)[3.02]; N1(imino)-N3[3.07]; N2(amino)-O2(carbonyl)[2.91]"
       bp_pars: [-0.16   0.05    0.03    -1.64   -16.84  0.00]
  34 .D0A0.A.DC.7.    .D0A0.B.DG.14.   C-G WC           19-XIX    cWW cW-W
       -153.4(anti) C3'-endo lambda=56.2; -162.2(anti) C3'-endo lambda=54.8
       d(C1'-C1')=10.52 d(N1-N9)=8.85 d(C6-C8)=9.78 tor(N1-C1'-C1'-N9)=-15.6
       H-bonds[3]: "O2(carbonyl)-N2(amino)[2.67]; N3-N1(imino)[2.81]; N4(amino)-O6(carbonyl)[2.85]"
       bp_pars: [0.42    -0.26   -0.10   2.69    -7.28   0.66]
  35 .D0A0.A.DC.8.    .D0A0.B.DG.13.   C-G WC           19-XIX    cWW cW-W
       -170.0(anti) C3'-endo lambda=57.0; -178.7(anti) C2'-exo lambda=52.7
       d(C1'-C1')=10.66 d(N1-N9)=8.96 d(C6-C8)=9.90 tor(N1-C1'-C1'-N9)=-5.4
       H-bonds[3]: "O2(carbonyl)-N2(amino)[2.74]; N3-N1(imino)[2.96]; N4(amino)-O6(carbonyl)[3.06]"
       bp_pars: [0.53    -0.13   -0.14   2.56    -6.75   2.31]

****************************************************************************
List of 8 multiplet(s)
   1 nts=3 ..A.DG.4.+..B.DC.17.+.B00A.A.G.10. [GCG]
   2 nts=3 ..A.DC.7.+..B.DG.14.+.D000.B.G.20. [CGG]
   3 nts=3 ..A.G.10.+.B000.A.DG.4.+.B000.B.DC.17. [GGC]
   4 nts=3 ..B.G.20.+.D0A0.A.DC.7.+.D0A0.B.DG.14. [GCG]
   5 nts=4 ..A.C.1.+..B.G.20.+.D0A0.A.DG.6.+.D0A0.B.DC.15. [CGGC]
   6 nts=4 ..A.DG.3.+..B.DC.18.+.B00A.A.G.10.+.B00A.B.C.11. [GCGC]
   7 nts=4 ..A.DG.6.+..B.DC.15.+.D000.A.C.1.+.D000.B.G.20. [GCCG]
   8 nts=4 ..A.G.10.+..B.C.11.+.B000.A.DG.3.+.B000.B.DC.18. [GCGC]

****************************************************************************
List of 4 helices
  helix#1[1] bps=10
    helical-axis[2.39(0.56)]:   0.910  -0.336  -0.241
                   point-one:  -5.968   2.594  13.365
                   point-two:  13.332  -4.536   8.252
   1 ..A.C.1.         ..B.G.20.        C-G WC           19-XIX    cWW cW-W
   2 ..A.DC.2.        ..B.DG.19.       C-G WC           19-XIX    cWW cW-W
   3 ..A.DG.3.        ..B.DC.18.       G-C WC           19-XIX    cWW cW-W
   4 ..A.DG.4.        ..B.DC.17.       G-C WC           19-XIX    cWW cW-W
   5 ..A.DC.5.        ..B.DG.16.       C-G WC           19-XIX    cWW cW-W
   6 ..A.DG.6.        ..B.DC.15.       G-C WC           19-XIX    cWW cW-W
   7 ..A.DC.7.        ..B.DG.14.       C-G WC           19-XIX    cWW cW-W
   8 ..A.DC.8.        ..B.DG.13.       C-G WC           19-XIX    cWW cW-W
   9 ..A.DG.9.        ..B.DC.12.       G-C WC           19-XIX    cWW cW-W
  10 ..A.G.10.        ..B.C.11.        G-C WC           19-XIX    cWW cW-W
  --------------------------------------------------------------------------
  helix#2[1] bps=2
    helical-axis[2.74(0.03)]:  -0.920   0.389  -0.051
                   point-one:  14.406   1.922  -9.270
                   point-two:  11.887   2.987  -9.409
   1 .B000.A.DG.3.    .B000.B.DC.18.   G-C WC           19-XIX    cWW cW-W
   2 .B000.A.DG.4.    .B000.B.DC.17.   G-C WC           19-XIX    cWW cW-W
  --------------------------------------------------------------------------
  helix#3[1] bps=3
    helical-axis[3.74(0.22)]:  -0.798  -0.062   0.600
                   point-one:  -3.749  16.576   9.104
                   point-two:  -9.825  16.103  13.669
   1 .D0A0.A.DG.6.    .D0A0.B.DC.15.   G-C WC           19-XIX    cWW cW-W
   2 .D0A0.A.DC.7.    .D0A0.B.DG.14.   C-G WC           19-XIX    cWW cW-W
   3 .D0A0.A.DC.8.    .D0A0.B.DG.13.   C-G WC           19-XIX    cWW cW-W
  --------------------------------------------------------------------------
  helix#4[1] bps=2
    helical-axis[2.87(0.04)]:  -0.801   0.320  -0.506
                   point-one:  -0.996   2.525  29.487
                   point-two:  -3.291   3.441  28.036
   1 .B00A.A.DG.9.    .B00A.B.DC.12.   G-C WC           19-XIX    cWW cW-W
   2 .B00A.A.G.10.    .B00A.B.C.11.    G-C WC           19-XIX    cWW cW-W

****************************************************************************
List of 4 stems
  stem#1[#1] bps=10
    helical-axis[2.39(0.56)]:   0.910  -0.336  -0.241
                   point-one:  -5.968   2.594  13.365
                   point-two:  13.332  -4.536   8.252
   1 ..A.C.1.         ..B.G.20.        C-G WC           19-XIX    cWW cW-W
   2 ..A.DC.2.        ..B.DG.19.       C-G WC           19-XIX    cWW cW-W
   3 ..A.DG.3.        ..B.DC.18.       G-C WC           19-XIX    cWW cW-W
   4 ..A.DG.4.        ..B.DC.17.       G-C WC           19-XIX    cWW cW-W
   5 ..A.DC.5.        ..B.DG.16.       C-G WC           19-XIX    cWW cW-W
   6 ..A.DG.6.        ..B.DC.15.       G-C WC           19-XIX    cWW cW-W
   7 ..A.DC.7.        ..B.DG.14.       C-G WC           19-XIX    cWW cW-W
   8 ..A.DC.8.        ..B.DG.13.       C-G WC           19-XIX    cWW cW-W
   9 ..A.DG.9.        ..B.DC.12.       G-C WC           19-XIX    cWW cW-W
  10 ..A.G.10.        ..B.C.11.        G-C WC           19-XIX    cWW cW-W
  --------------------------------------------------------------------------
  stem#2[#2] bps=2
    helical-axis[2.74(0.03)]:  -0.920   0.389  -0.051
                   point-one:  14.406   1.922  -9.270
                   point-two:  11.887   2.987  -9.409
   1 .B000.A.DG.3.    .B000.B.DC.18.   G-C WC           19-XIX    cWW cW-W
   2 .B000.A.DG.4.    .B000.B.DC.17.   G-C WC           19-XIX    cWW cW-W
  --------------------------------------------------------------------------
  stem#3[#3] bps=3
    helical-axis[3.74(0.22)]:  -0.798  -0.062   0.600
                   point-one:  -3.749  16.576   9.104
                   point-two:  -9.825  16.103  13.669
   1 .D0A0.A.DG.6.    .D0A0.B.DC.15.   G-C WC           19-XIX    cWW cW-W
   2 .D0A0.A.DC.7.    .D0A0.B.DG.14.   C-G WC           19-XIX    cWW cW-W
   3 .D0A0.A.DC.8.    .D0A0.B.DG.13.   C-G WC           19-XIX    cWW cW-W
  --------------------------------------------------------------------------
  stem#4[#4] bps=2
    helical-axis[2.87(0.04)]:  -0.801   0.320  -0.506
                   point-one:  -0.996   2.525  29.487
                   point-two:  -3.291   3.441  28.036
   1 .B00A.A.DG.9.    .B00A.B.DC.12.   G-C WC           19-XIX    cWW cW-W
   2 .B00A.A.G.10.    .B00A.B.C.11.    G-C WC           19-XIX    cWW cW-W

****************************************************************************
List of 1 lone WC/wobble pair(s)
  -1 .D000.A.C.1.     .D000.B.G.20.    C-G WC           19-XIX    cWW cW-W

****************************************************************************
>100d.py-A #1 DNA[19]/RNA[5]* with 24 nts
CCGGCGCCGGGGCGCCGGGGCCGC
((((((((((((..(..(((((..
>100d.py-B #2 DNA[19]/RNA[6]* with 25 nts
CCGGCGCCGGCCGGGCCGGGCGGCC
))))))))))))..))).)))....

****************************************************************************
List of 5 additional files generated with this DSSR run
   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-torsions.dat -- Torsion angles and backbone(BI/BII) classification

Note the format of nt id string is now:

model-number.seqid.chain-id.nt-name.nt-number.insertion-code

Please have a try and report back how it goes.

Xiang-Jun

Title: Re: dealing with symmetrics
Post by: auffinger 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

Title: Re: dealing with symmetrics
Post by: xiangjun on September 16, 2013, 12:30:30 pm

Hi Pascal,

Thanks for your following up. As of beta-r19-on-20130819, I have "removed the segid info from nucleotide id-string by default" (see the release note). As you already noticed, segid is not in PDB format v3, nor is it in PDBx/mmCIF. It thus makes sense to me to remove it from the DSSR default output, since it would empty in the majority of cases. However, you can get what to desire by specifying the --segid option explicitly.

HTH,

Xiang-Jun

Title: Re: dealing with symmetrics
Post by: auffinger 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

Title: Re: dealing with symmetrics
Post by: xiangjun on September 18, 2013, 03:17:13 pm

Hi Pascal,

I've updated DSSR to beta-r23-on-20130918 on the download page. Please verify and report back if it fixes the problem you experienced.

As a general rule, it helps that users follow up timely on a case-by-case basis rather than post back only when they have a new request or meet another problem.

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University