Topics

26

General discussions (Q&As) / non planar base pairs

« on: April 17, 2010, 01:19:28 pm »

Dear Xiang-Jun,

Another interrogation related to 3DNA. We came accross a strange base pair selected by find_pair, the base looks almost othogonal and this, although not frequent, is not a unique case (this base pair involves symmetry related residues). We used find_pair -p on a modified PDB file of the 1DC0 structure with following parameters:
Base-pair criteria used:   3.35   0.00  15.00   1.50  65.00   4.50   7.50 [ O N].

In which way should we change these parameters in order to eliminate such base pairs (thought stagger=1.5 would do)?

see attached files,

Best regards,

Pascal

27

General discussions (Q&As) / find_pair and HETATM

« on: March 22, 2010, 01:48:16 pm »

Dear Xiang-Jun,

Just found out that for some base pairs, find_pair extracts some additional atoms (CA, K, TL, MG among others) and also complete modified residues like in 1MO5 (bp 12) and 2PIS (bp 9) (see attached files). Is that how it should be. Did we miss an option or misunderstand something ? This does not occur with the -a option, yet info related to modified residues are then lost.

Thanks for your help,

Pascal

28

General discussions (Q&As) / findpair -p and -z options

« on: March 11, 2010, 11:08:41 am »

Dear Xiang-Jun,

Recently, we tried to use find_pair with the -p option that gives more complete listings of base pairs. Yet, the output of find_pair with the -p option seems not comptatible with analyze. Hence we tried to convert the extended output of findpair into the simplier one, without any clue about where to get the right info about the (|, x, and +) signs associated with the (0, 1, 9) numbers (helix breaks ?). is there any easier way, to make analyze work on the complex output of find_pair ?

Also,

    1    1  197  344 ....>C:...1_:[.DT]T-**+-A[.DA]:..21_:D<....
             T+A     -0.64    3.35    1.34  -23.31    0.25  -70.84
             T+A [2]  N3 - N7  2.76  O4 - N6  2.82
                    parallel cis cis
            +++     69.2     74.1     23.3     73.2   -109.2   -127.6
         3.66    1.34   23.31    6.65    4.51   -9.93   53.38   21.36

what do the three +++ mean here as well as other undocumented thinks.

Thanks for help,

Kind regards,

Pascal

29

General discussions (Q&As) / Baselist.dat

« on: April 08, 2008, 11:45:41 am »

Dear Xiang-Jun,

We recently experienced a pb with the file baselist.dat. This file contains all the name exceptions that are contained in a PDB file. If a residue name for a modified base is not present in this file, the entire nucleic acid structure is skipped by 3DNA. Hence, we added residue names by hand to this file (see attached baselist1.dat) and it worked  up to a certain point. Lately, we tried with the (attached) file baselist2.dat and the program crashed giving a "too many arguments" message. Are there too many residue names in this file or did something else go wrong ?

Thanks for your answer,

and kind regards,

Pascal

30

General discussions (Q&As) / SwS : Solvation web Service for nucleic acids

« on: March 17, 2008, 10:53:24 am »

Hi Xiang-Jun,

Just visited your 2.0 site. Looks good. Apparently you improved the algorithms for detecting base pairs. Will this change something for us  (with SwS I mean - at http://tatooine.u-strasbg.fr/~sws/SwS.html). Although, since our pre-processor is strongly linked to the 1.5 file formats, we were just wondering if something changed at this level and eventually what type of adaptations would be necessary.

Kind regards,

Pascal

31

General discussions (Q&As) / base pair stagger

« on: November 24, 2006, 12:20:05 pm »

Dear Xiang-Jun,

I am having a little problem with understanding your maximum vertical
distance between base origins since I was unable to find a description of
how these base origins are calculated. Could you give me a hint?

In fact, we realized that with the 2.5 criteria you propose we are taking
into account base pairs like the one attached to this mail (G-U pair) that
should obviously be excluded. The stagger value for this base pair is close
to 2.0 which is a quite high value. Could you also help me to find a
reference related to how this stagger parameter is caculated?

Pascal


REMARK    3DNA (v1.5, Nov. 2002) by Xiang-Jun Lu at Wilma K. Olson's Lab.
ATOM      1  P     G 0 257       4.449   6.613  -2.015  1.00 81.87           P  
ATOM      2  O5'   G 0 257       2.993   6.752  -1.388  1.00 80.67           O  
ATOM      3  C5'   G 0 257       2.072   7.748  -1.869  1.00 76.88           C  
ATOM      4  C4'   G 0 257       0.649   7.294  -1.649  1.00 74.57           C  
ATOM      5  O4'   G 0 257       0.487   5.980  -2.245  1.00 73.84           O  
ATOM      6  C3'   G 0 257       0.221   7.086  -0.203  1.00 72.87           C  
ATOM      7  O3'   G 0 257      -0.192   8.298   0.419  1.00 72.75           O  
ATOM      8  C2'   G 0 257      -0.937   6.119  -0.359  1.00 72.75           C  
ATOM      9  O2'   G 0 257      -2.113   6.758  -0.806  1.00 72.14           O  
ATOM     10  C1'   G 0 257      -0.405   5.206  -1.464  1.00 73.40           C  
ATOM     11  N9    G 0 257       0.326   4.070  -0.908  1.00 73.88           N  
ATOM     12  C8    G 0 257       1.684   3.842  -0.935  1.00 74.09           C  
ATOM     13  N7    G 0 257       2.029   2.744  -0.318  1.00 74.52           N  
ATOM     14  C5    G 0 257       0.829   2.211   0.136  1.00 73.68           C  
ATOM     15  C6    G 0 257       0.563   1.028   0.876  1.00 72.05           C  
ATOM     16  O6    G 0 257       1.363   0.187   1.294  1.00 72.32           O  
ATOM     17  N1    G 0 257      -0.797   0.873   1.122  1.00 70.92           N  
ATOM     18  C2    G 0 257      -1.780   1.742   0.715  1.00 71.57           C  
ATOM     19  N2    G 0 257      -3.039   1.429   1.056  1.00 70.83           N  
ATOM     20  N3    G 0 257      -1.547   2.843   0.026  1.00 72.99           N  
ATOM     21  C4    G 0 257      -0.232   3.014  -0.226  1.00 73.83           C  
ATOM     22  O1P   G 0 257       5.102   7.940  -1.901  1.00 82.54           O  
ATOM     23  O2P   G 0 257       5.112   5.414  -1.434  1.00 81.39           O  
ATOM     24  P     U 0 253      -4.704  -6.982  -0.337  1.00 65.64           P  
ATOM     25  O5'   U 0 253      -4.084  -5.768  -1.160  1.00 69.18           O  
ATOM     26  C5'   U 0 253      -4.932  -4.872  -1.903  1.00 73.30           C  
ATOM     27  C4'   U 0 253      -4.097  -3.875  -2.669  1.00 75.72           C  
ATOM     28  O4'   U 0 253      -3.480  -2.935  -1.751  1.00 75.82           O  
ATOM     29  C3'   U 0 253      -2.916  -4.450  -3.430  1.00 77.91           C  
ATOM     30  O3'   U 0 253      -3.273  -5.082  -4.654  1.00 79.93           O  
ATOM     31  C2'   U 0 253      -2.044  -3.218  -3.623  1.00 77.94           C  
ATOM     32  O2'   U 0 253      -2.524  -2.372  -4.648  1.00 78.00           O  
ATOM     33  C1'   U 0 253      -2.221  -2.528  -2.269  1.00 77.57           C  
ATOM     34  N1    U 0 253      -1.164  -2.892  -1.311  1.00 78.25           N  
ATOM     35  C2    U 0 253      -0.231  -1.923  -0.983  1.00 79.12           C  
ATOM     36  O2    U 0 253      -0.261  -0.790  -1.435  1.00 79.66           O  
ATOM     37  N3    U 0 253       0.745  -2.331  -0.105  1.00 79.61           N  
ATOM     38  C4    U 0 253       0.884  -3.576   0.465  1.00 79.00           C  
ATOM     39  O4    U 0 253       1.841  -3.800   1.210  1.00 79.06           O  
ATOM     40  C5    U 0 253      -0.124  -4.518   0.086  1.00 79.19           C  
ATOM     41  C6    U 0 253      -1.090  -4.153  -0.765  1.00 78.38           C  
ATOM     42  O1P   U 0 253      -5.725  -7.656  -1.182  1.00 64.76           O  
ATOM     43  O2P   U 0 253      -3.581  -7.769   0.226  1.00 65.63           O  
HETATM   44  O   HOH  4525       6.320   2.815  -0.315  1.00 66.90           O  
END