Messages

76

General discussions (Q&As) / Re: find_pair and HETATM

« on: April 14, 2010, 08:59:29 am »

Dear Xiang-Jun,

Just a few words to let you know that, still, with the -attach options, some HETATM remain attached to the base pair as in one bp of 1VBZ (barium atom) - see picture. We should be able to workaround this for now.

Kind regards,

Pascal

77

General discussions (Q&As) / Re: find_pair and HETATM

« on: April 12, 2010, 09:47:47 am »

Dear Xiang-Jun,

Well, the .ana output does not apparently provide the column filed with | and x characters that is used for calculating stackings and other base pair step related infos (it seems to us). This results in an output from analyze in which some sections are just filled with zeros. At a later point we will probably need this info and forget our workaround. The workaround we wrote in perl converts the output from "find_pair -p" by placing indiscriminately | characters in this column. Not perfect indeed - its a workaround, but works at least for our purpose.

As for the RN9-YN1 and RC8-YC69 columns, you are right and we noticed that the info are correct, but the columns are misslabeled and that is something that might trouble other users. May be you would like to change at a later point the labeling of these columns to a lengthy text or something simpler with a note explaining what it means (much more coherent and satisfactory). Again, yes, the data are correct, no doubt about that.

pascal

78

General discussions (Q&As) / Re: find_pair and HETATM

« on: April 09, 2010, 08:50:19 am »

Hi Xiang-Jun,

Finally we tested your option -attach that works really fine. A lot easier for us. now! The .ana output looks less interesting to us than our workaround since it s lacking some info that we get by rewriting the find_pair output with -pz to a new output readable by analyze. At a later stage, it would be nice to have a complete output for analyze comming out from "find_pair -pz".

Was just also looking at the RN9-YN1 and RC8-YC6 info you provide in the analyze output. The labeling of this columns seems not appropriate since you do not consider the YY and RR base pairs occurrences, do you ?. The YN1-YN1 and RN9-RN9 columns are missing apparently. From my point of view, the C1'-C1' and the two lambdas provide all the needed info.

Best wishes and thanks again for your help,

Pascal

79

General discussions (Q&As) / Re: find_pair and HETATM

« on: March 29, 2010, 06:49:45 am »

Hi Xiang-Jun,

We use Linux Ubuntu 8.04 LTS. Thanks for your help,

Pascal

80

General discussions (Q&As) / Re: find_pair and HETATM

« on: March 25, 2010, 07:10:46 am »

Dear Xiang-Jun,

Again, we appreciate your dedication to 3DNA and this program is a the ground on which a large part of our research evolves. As for "find_pair -p", we wrote a workaround (that is just a workaround) since we cannot translate everything (different info in both findpair outputs). If you do that, it would be certainly much nicer and accurate and benefit to ourselfs (certainly) and others (probably). Thanks.

Best regards,

Pascal

81

General discussions (Q&As) / Re: find_pair and HETATM

« on: March 24, 2010, 06:37:57 am »

Dear Xiang-Jun,

Thanks for your reply. I understand better what you intended to do. This is, as you wrote, undocumented and therefore puzzling when one discovers it, although probably very useful when one is aware of the bias you chose. Indeed, an option in find_pair, related to this issue would be really welcome and add more flexibility to 3DNA. Getting an updated version is great news for us and we are waiting for it.
Regarding our last post, we would also really appreciate if you could at one point consider providing an output for "find_pair -p" (using the -p option) that could be run through analyze (its not the case right now). This would be also more than helpful for us. Yet, I understand that you are really busy combining several jobs.

Thanks for being so reactive,

Kind regards,

Pascal

82

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

83

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

« on: March 14, 2010, 05:30:42 pm »

Dear Mauricio,

Thanks your repy, but yes, I am aware of this great BPS site and hope you are also aware about our http://tatooine.u-strasbg.fr/~sws/SwS.html site that is currently undergoing a big restructuration. I am still surprised to find out how much there is still to say about base pairs.

Cheers,

Pascal

84

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

85

w3DNA -- web interface to 3DNA / update frequency

« on: November 23, 2009, 06:05:28 am »

Dear All,

Thanks for setting up w3DNA, a really great tool. Just wondering with which frequency the new PDB structures are made available through your web service. A meekly or monthly update would be really appreciable.

Kind regards,

Pascal

86

General discussions (Q&As) / Re: Baselist.dat

« on: April 10, 2008, 12:16:27 pm »

Thanks Xiang-Jun,

Of course, we could wait for the new release but, in the mean time, do you think you could manage to send us a linux version without this size limitation ?

Pascal

87

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

88

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

89

General discussions (Q&As) /

« on: November 27, 2006, 06:35:05 am »

Hi Xiang-Jun,

I understand perfectly your point altough, personnally, I do think that using a h-bond distance above 3.5A is considerably exagerated, but that is an other topic.

Yes, I use the "misc_3dna.par" file. However, the aim of my question was to understand how you calulate this "vertical distance between base pair origins". Is this the same as this stagger parameter (probably not). Could you then tell me why you do not use the stagger parameter instead.

This is also why I wanted to know how you determine the "base origin". I already knew how you determine the "base pair origin".

Best regards,

Pascal

90

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