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Messages - xiangjun

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1
Try the --loop=with-stems option.

Xiang-Jun

2
RNA structures (DSSR) / Re: How to look for abasic site using DSSR
« on: April 26, 2017, 01:56:41 pm »
Hi Honglue,

As shown in Fig.1 (see below) of the DSSR paper, "Nucleotides are recognized using standard atom names and base planarity." Since abasic sites (e.g., HPD18 in chain C of PDB id 1l2c) do not have proper base atoms, they are not recognized as nucleotides by DSSR to begin with. Naturally, they do not appear in later analysis results of DSSR output. This is just the way DSSR works and you may take it as a deficiency. Please let me know if you have a better way to handle such cases.



Hope this clarifies your confusions.

Xiang-Jun

3
DNA-protein interactions (SNAP) / Re: Unrecognized interactions
« on: April 11, 2017, 11:49:33 am »
Hi David,

Thank you so much for your feedback! As you know, the SNAP program is still in beta, so I'm completely open to constructive suggestions like yours.

Quote
If I understand correctly, the section "List of X nucleotide/amino-acid interactions" while using --type=either should include all interactions in the respective protein--DNA complex PDB structure which fall into the chosen inter-atomic distance cut-off ? And choosing --type=base or --type=backbone should report only the interactions of amino acid residues which interact with the DNA bases or DNA backbone, respectively, but not with the other one ?

  • --type=base -- must have contacts with base atoms, may contact DNA/RNA backbone
  • --type=backbone -- must have contacts with backbone atoms, may contact base
  • --type=either -- must have contacts with base atoms or DNA/RNA backbone, may contact both
  • --type=both -- must have contacts with base atoms and DNA/RNA backbone

Some of the interactions you're interested may be considered vdw contacts or hydrophobic interactions, which are currently not listed under the various H-bonding sections.

I understand the crucial importance of hydrophobic interactions in protein folding, and protein-DNA/RNA recognition. However, I've not been able to find a pragmatic algorithm, other than simple (carbon/carbon) distances, to identify them given a PDB structure. I've been reading some papers on the topic recently. Do you have any suggestion on must-read papers?

I'll update SNAP to a new release by next week. In the meantime, please feel free to communicate back your ideas on how SNAP could be made most useful from a user's perspective.

Best regards,

Xiang-Jun

4
DNA-protein interactions (SNAP) / Re: Unrecognized interactions
« on: April 10, 2017, 11:54:05 am »
Hi David,

Please try SNAP with the "--type=either" option. By default, only protein interactions with BASE atoms are reported. Using 'either' would also include backbone interactions. I'll document this option in the coming release of SNAP.

Please have a try and report back if that helps.

Xiang-Jun

5
General discussions (Q&As) / Re: Minor and major grove calculation
« on: April 04, 2017, 11:10:25 pm »
Please upgrade 3DNA v2.3, that's the latest version. See $X3DNA/doc/groove-widths.pdf for the original El Hassan & Calladine reference.

Xiang-Jun

6
With now.pdb, and 3DNA v2.3 (the current version):

Code: [Select]
find_pair now.pdb now.inp
You will see diagnostic (not error) message like the following:

Code: [Select]
Match ' DM' to 'c' for residue  DM    2  on chain A [#2]
    check it & consider to add line ' DM     c' to file <baselist.dat>

The main output file now.inp has the following content:

Code: [Select]
now.pdb
now.out
    2         # duplex
   40         # number of base-pairs
    1     1    # explicit bp numbering/hetero atoms
    1    40   0 #    1 | ...1>A:...1_:[.DG]G-----c[.DM]:..20_:A<...1   0.40   0.01  25.87   9.03  -3.28
    2    39   0 #    2 | ...1>A:...2_:[.DM]c-----G[.DG]:..19_:A<...1   0.35   0.10  16.33   8.95  -3.63
    3    38   0 #    3 | ...1>A:...3_:[.DG]G-----c[.DM]:..18_:A<...1   0.62   0.58  17.77   8.90  -2.32
    4    37   0 #    4 | ...1>A:...4_:[.DM]c-----G[.DG]:..17_:A<...1   1.05   1.03  21.25   9.11  -0.83
    5    36   0 #    5 | ...1>A:...5_:[.DG]G-----c[.DM]:..16_:A<...1   0.75   0.67   5.95   9.04  -2.63
    6    35   0 #    6 | ...1>A:...6_:[.DM]c-----G[.DG]:..15_:A<...1   0.20   0.15   8.76   9.07  -4.06
    7    34   0 #    7 | ...1>A:...7_:[.DG]G-----c[.DM]:..14_:A<...1   0.65   0.63  22.39   9.00  -1.98
    8    33   0 #    8 | ...1>A:...8_:[.DM]c-----G[.DG]:..13_:A<...1   0.57   0.31  20.15   8.93  -2.81
    9    32   0 #    9 | ...1>A:...9_:[.DG]G-----c[.DM]:..12_:A<...1   1.04   0.55  20.34   8.80  -1.84
   10    31   0 #   10 | ...1>A:..10_:[.DM]c-----G[.DG]:..11_:A<...1   0.42   0.32  30.85   9.18  -2.40
   11    30   0 #   11 | ...1>A:..11_:[.DG]G-----c[.DM]:..10_:A<...1   0.31   0.24  20.12   9.02  -3.20
   12    29   0 #   12 | ...1>A:..12_:[.DM]c-----G[.DG]:...9_:A<...1   0.33   0.23  17.73   8.96  -3.31
   13    28   0 #   13 | ...1>A:..13_:[.DG]G-----c[.DM]:...8_:A<...1   0.11   0.02   4.82   8.99  -4.60
   14    27   0 #   14 | ...1>A:..14_:[.DM]c-----G[.DG]:...7_:A<...1   0.25   0.05  15.58   9.00  -3.87
   15    26   0 #   15 | ...1>A:..15_:[.DG]G-----c[.DM]:...6_:A<...1   0.86   0.64  11.46   9.23  -2.29
   16    25   0 #   16 | ...1>A:..16_:[.DM]c-----G[.DG]:...5_:A<...1   0.08   0.03  17.21   8.95  -4.00
   17    24   0 #   17 | ...1>A:..17_:[.DG]G-----c[.DM]:...4_:A<...1   0.59   0.37  16.52   8.98  -2.84
   18    23   0 #   18 | ...1>A:..18_:[.DM]c-----G[.DG]:...3_:A<...1   0.13   0.13  17.26   9.12  -3.75
   19    22   0 #   19 | ...1>A:..19_:[.DG]G-----c[.DM]:...2_:A<...1   0.31   0.26  11.89   9.12  -3.57
   20    21   9 #   20 x ...1>A:..20_:[.DM]c-----G[.DG]:...1_:A<...1   0.45   0.38  28.30   9.12  -2.38
   41    80   0 #   21 | ...1>B:...1_:[.DG]G-----c[.DM]:..20_:B<...1   0.45   0.13  21.26   8.91  -3.23
   42    79   0 #   22 | ...1>B:...2_:[.DM]c-----G[.DG]:..19_:B<...1   0.46   0.32  24.76   9.07  -2.66
   43    78   0 #   23 | ...1>B:...3_:[.DG]G-----c[.DM]:..18_:B<...1   0.25   0.20  12.01   9.01  -3.75
   44    77   0 #   24 | ...1>B:...4_:[.DM]c-----G[.DG]:..17_:B<...1   0.37   0.32  19.75   9.13  -3.00
   45    76   0 #   25 | ...1>B:...5_:[.DG]G-----c[.DM]:..16_:B<...1   0.20   0.13  19.64   9.12  -3.56
   46    75   0 #   26 | ...1>B:...6_:[.DM]c-----G[.DG]:..15_:B<...1   1.01   1.01  20.99   9.15  -0.93
   47    74   0 #   27 | ...1>B:...7_:[.DG]G-----c[.DM]:..14_:B<...1   0.40   0.37  18.39   9.23  -2.95
   48    73   0 #   28 | ...1>B:...8_:[.DM]c-----G[.DG]:..13_:B<...1   0.88   0.46  20.27   9.05  -2.19
   49    72   0 #   29 | ...1>B:...9_:[.DG]G-----c[.DM]:..12_:B<...1   0.92   0.84  21.58   8.98  -1.31
   50    71   0 #   30 | ...1>B:..10_:[.DM]c-----G[.DG]:..11_:B<...1   0.92   0.89  16.24   9.15  -1.49
   51    70   0 #   31 | ...1>B:..11_:[.DG]G-----c[.DM]:..10_:B<...1   0.33   0.15  18.78   8.97  -3.43
   52    69   0 #   32 | ...1>B:..12_:[.DM]c-----G[.DG]:...9_:B<...1   0.29   0.13  25.28   9.03  -3.20
   53    68   0 #   33 | ...1>B:..13_:[.DG]G-----c[.DM]:...8_:B<...1   0.57   0.47  27.56   8.80  -2.10
   54    67   0 #   34 | ...1>B:..14_:[.DM]c-----G[.DG]:...7_:B<...1   0.62   0.56  20.66   9.09  -2.24
   55    66   0 #   35 | ...1>B:..15_:[.DG]G-----c[.DM]:...6_:B<...1   0.20   0.08  11.63   9.19  -4.05
   56    65   0 #   36 | ...1>B:..16_:[.DM]c-----G[.DG]:...5_:B<...1   0.58   0.51  16.11   9.22  -2.60
   57    64   0 #   37 | ...1>B:..17_:[.DG]G-----c[.DM]:...4_:B<...1   0.91   0.20   8.59   8.75  -3.25
   58    63   0 #   38 | ...1>B:..18_:[.DM]c-----G[.DG]:...3_:B<...1   0.88   0.72  11.69   9.01  -2.10
   59    62   0 #   39 | ...1>B:..19_:[.DG]G-----c[.DM]:...2_:B<...1   0.74   0.70  29.13   8.88  -1.40
   60    61   0 #   40 | ...1>B:..20_:[.DM]c-----G[.DG]:...1_:B<...1   0.17   0.10  19.09   9.01  -3.68
##### Base-pair criteria used:     4.00     0.00    15.00     2.50    65.00     4.50     7.80 [ O N]
##### 0 non-Watson-Crick base-pairs, and 2 helices (0 isolated bps)
##### Helix #1 (20): 1 - 20
##### Helix #2 (20): 21 - 40

So 3DNA is performing as expected.

Xiang-Jun

7
Again, providing an example PDB file would make things much clearer.

Which version of 3DNA are you using? Methylated cytosine can certainly be handled automatically. However, without a reproducible example, I cannot help any further.

Xiang-Jun

8
It'd be very helpful to simply attach a PDB file that illustrates unambiguously what the problem is and how you fixed it.

Xiang-Jun

9
Hi Basilio,

Generally speaking, 3DNA can handle non-standard bases quite well. For your case, please provide a reproducible example so other can see exactly where the problem is.

Xiang-Jun

10
RNA structures (DSSR) / Re: atom-base capping
« on: April 04, 2017, 10:06:24 am »
Try --a2base-vd=4, for example.

Xiang-Jun

11
Quote
I could see there is not a difference between a pair A-T and G-C.

Good catch! The table was compiled by combining A–T and G–C pairs together. In reality, there is some difference in propeller between the two pairs: A–T has slightly larger (more negative) propeller than G–C. At this moment, I cannot trace back the original data I used for Table 3 of the report.

Xiang-Jun

12
The report "A standard reference frame for the description of nucleic acid base-pair geometry." [the original PDF at the NDB server] contains a table (Table 3) that lists average values and dispersion of base-pair parameters in high resolution A-and B-DNA crystal structures. Among which, propeller is included.

HTH,

Xiang-Jun

13
Quote
it only gives me hydrogen bonds in rna-not between protein and rna.

By default, the DSSR --get-hbond option outputs only H-bonds within nucleic acids. You can get additional protein-RNA H-hbonds by specifying --get-hbond=at-interface.

As mentioned several times in the Forum, the H-bond identification algorithm in DSSR (and SNAP) has been designed to make DSSR fully self-contained. While it fulfills its role well, it may not be as sophisticated as dedicated programs such as HBPLUS and HBExplore. Please keep this (possible) limitation in mind.

Xiang-Jun

14
RNA structures (DSSR) / Re: x3dna-dssr installation
« on: March 27, 2017, 10:56:50 pm »
Note: DSSR is fully self-contained, and independent of 3DNA v2.3. DSSR (the x3dna-dssr executable) does not need to be in the $X3DNA folder at all. It can be put anywhere in your PATH, as documented in the User Manual.

Xiang-Jun

15
RNA structures (DSSR) / Re: x3dna-dssr installation
« on: March 27, 2017, 08:07:24 pm »
Quote
I was able to run x3dna-dssr after following your advice. Thank you very much!

Glad to hear the installation problem has been solved. From the above info, it's hard to guess what route you took. By design, it should be straightforward to get DSSR up and running. That's been the case in my experience over the past few years. Your scenario worths attention for the benefit of other new DSSR users. Could you please detail how you solve the DSSR installation problem, step-by-step, from a beginner's perspective?

Quote
I have a quick question about hydrogen bonds-can the program find hydrogen bonds between protein and rna (a docked system)? I have tried using get-hbonds command. However, it only gives me hydrogen bonds in rna-not between protein and rna.

This question has nothing to do with the current topic on "x3dna-dssr installation". Please start a new thread.

Hopefully, I've made my points clear.

Xiang-Jun

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Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.