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91
RNA structures (DSSR) / discarded nucleotides in json output
« Last post by ICdB on March 04, 2018, 08:36:01 am »
Hi,

First, many thanks for your great software suite. It is a real pleasure to work with such complete and convenient outputs for my parsing purposes. I am a strong believer in collaboration in methods development trough connectible building blocs, and it is nice to have others with such view in the RNA-modeling field  :)

I am building specific structural fragment libraries for RNA docking, and I try to parse dssr json outputs to automatically keep track of my fragments characteristics (2D structure, interactions ...). For this, I need to now which nucleotides were discarded because of e.g. weird geometry. As I see it, a "&" is inserted in the "bseq" entry for chain breaks. But I can't find any indication of if a nucleotide was discarded or the break was already present in the input pdb, and retrieving it by comparing bseq to the input sequence can be ambiguous.
I am considering using the "Summary of structural features of xx nucleotides" in the text output, by running dssr w. and wo. the "--json" option. Is there a dssp option I could use to get the info directly from the json output and avoid double work (as I am analysing thousands of pdb files)?

Thanks in advance for your help,
Isaure C. de Beauchene

PS: I'm using version v1.7.2-2017nov20
92
General discussions (Q&As) / Re: base/nucleotide recognition
« Last post by cys on February 28, 2018, 06:45:06 pm »
I deleted X3DNA and reinstalled it. It's now working for this example.
93
General discussions (Q&As) / Re: base/nucleotide recognition
« Last post by xiangjun on February 28, 2018, 06:20:03 pm »
Once again, reproducibility is the key, even for this presumably simple case.
94
General discussions (Q&As) / Re: base/nucleotide recognition
« Last post by cys on February 28, 2018, 06:07:34 pm »
It doesn't work for me. I'll continue to look at it. Thanks.
95
General discussions (Q&As) / Re: base/nucleotide recognition
« Last post by xiangjun on February 28, 2018, 05:08:06 pm »
Let your new PDB file called "AT-new.pdb", here is what I got:

Code: [Select]
# find_pair AT-new.pdb
AT-new.pdb
AT-new.out
    2         # duplex
    1         # number of base-pairs
    1     1    # explicit bp numbering/hetero atoms
    1     2   1 #    1 + ....>A:...1_:[.DA]A-----T[.DT]:...8_:B<....   0.12   0.02  16.77   8.81  -4.01
##### 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 1 helix (1 isolated bp)
##### Helix #1 (1): 1

# x3dna-dssr -i=AT-new.pdb
List of 1 base pair
     nt1            nt2            bp  name        Saenger   LW   DSSR
   1 A.DA1          B.DT8          A-T WC          20-XX     cWW  cW-W
...

3DNA/DSSR are working as expected.
96
General discussions (Q&As) / Re: base/nucleotide recognition
« Last post by cys on February 28, 2018, 05:02:56 pm »
I swapped the C6 and C5M coordinates.

TITLE       
REMARK   
ATOM      1  O5'  DA A   1       3.324  -6.828   6.718  1.00 00.00           O 
ATOM      2  C5'  DA A   1       4.571  -7.209   6.133  1.00 00.00           C 
ATOM      3  C4'  DA A   1       4.756  -6.460   4.821  1.00 00.00           C 
ATOM      4  O4'  DA A   1       3.839  -6.953   3.812  1.00 00.00           O 
ATOM      5  C3'  DA A   1       4.487  -4.946   4.924  1.00 00.00           C 
ATOM      6  O3'  DA A   1       5.309  -4.203   4.005  1.00 00.00           O 
ATOM      7  C2'  DA A   1       3.038  -4.823   4.482  1.00 00.00           C 
ATOM      8  C1'  DA A   1       2.864  -5.975   3.475  1.00 00.00           C 
ATOM      9  N9   DA A   1       1.522  -6.566   3.524  1.00 00.00           N 
ATOM     10  C8   DA A   1       0.887  -7.103   4.638  1.00 00.00           C 
ATOM     11  N7   DA A   1      -0.373  -7.436   4.411  1.00 00.00           N 
ATOM     12  C5   DA A   1      -0.582  -7.109   3.081  1.00 00.00           C 
ATOM     13  C6   DA A   1      -1.753  -7.098   2.272  1.00 00.00           C 
ATOM     14  N6   DA A   1      -2.974  -7.451   2.709  1.00 00.00           N 
ATOM     15  N1   DA A   1      -1.610  -6.674   0.986  1.00 00.00           N 
ATOM     16  C2   DA A   1      -0.409  -6.249   0.543  1.00 00.00           C 
ATOM     17  N3   DA A   1       0.733  -6.141   1.234  1.00 00.00           N 
ATOM     18  C4   DA A   1       0.587  -6.578   2.501  1.00 00.00           C 
ATOM    166  O5'  DT B   8      -7.388  -3.499  -4.415  1.00 00.00           O 
ATOM    167  C5'  DT B   8      -6.648  -2.446  -5.053  1.00 00.00           C 
ATOM    168  C4'  DT B   8      -5.222  -2.934  -5.255  1.00 00.00           C 
ATOM    169  O4'  DT B   8      -4.667  -3.316  -3.975  1.00 00.00           O 
ATOM    170  C3'  DT B   8      -5.070  -4.167  -6.164  1.00 00.00           C 
ATOM    171  O3'  DT B   8      -3.796  -4.040  -6.799  1.00 00.00           O 
ATOM    172  C2'  DT B   8      -5.093  -5.322  -5.159  1.00 00.00           C 
ATOM    173  C1'  DT B   8      -4.324  -4.708  -3.988  1.00 00.00           C 
ATOM    174  N1   DT B   8      -4.607  -5.287  -2.674  1.00 00.00           N 
ATOM    175  C2   DT B   8      -3.512  -5.650  -1.875  1.00 00.00           C 
ATOM    176  O2   DT B   8      -2.343  -5.529  -2.250  1.00 00.00           O 
ATOM    177  N3   DT B   8      -3.840  -6.157  -0.640  1.00 00.00           N 
ATOM    178  C4   DT B   8      -5.115  -6.385  -0.132  1.00 00.00           C 
ATOM    179  O4   DT B   8      -5.262  -6.893   0.994  1.00 00.00           O 
ATOM    180  C5   DT B   8      -6.216  -5.990  -1.010  1.00 00.00           C 
ATOM    181  C5M  DT B   8      -7.630  -6.227  -0.557  1.00 00.00           C 
ATOM    182  C6   DT B   8      -5.907  -5.447  -2.226  1.00 00.00           C 
END













97
General discussions (Q&As) / Re: base/nucleotide recognition
« Last post by xiangjun on February 28, 2018, 04:58:16 pm »
Again, show exactly what you did so other can reproduce the problem.
98
General discussions (Q&As) / Re: base/nucleotide recognition
« Last post by cys on February 28, 2018, 04:54:46 pm »
If you make the coordinate swap does it detect the pair? I've made the swap, but this one pair is still not detected. All the other pairs in the larger duplex that this pair was extracted from are detected, including an unnatural base pair that I added to the baselist.dat file. Looking at the misc_3dna.par file it seems the pairing parameters are generous.
99
General discussions (Q&As) / Re: base/nucleotide recognition
« Last post by cys on February 28, 2018, 04:11:34 pm »
Thanks. Sorry for the trouble. I don't own a viewer that depicts the native pdb file names at present.
100
General discussions (Q&As) / Re: base/nucleotide recognition
« Last post by xiangjun on February 28, 2018, 03:06:59 pm »
Thanks for attaching a PDB file that illustrates the problem. The issue is due to erroneous atom names for B.DT8. The C6 atom should be in the six-membered ring, whilst the C5M is the methyl-group attached to C5. In you AT.pdb file, the C6 and C5M atoms are swapped. See the attached image.

Xiang-Jun
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.