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Questions and answers => General discussions (Q&As) => Topic started by: cys on February 28, 2018, 02:19:12 pm

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Title: base/nucleotide recognition
Post by: cys on February 28, 2018, 02:19:12 pm

I would like to ask how to adjust the recognition parameters as I'm running into problems with x3dna and dssr "missing" a TA base pair (x3DNA) and a T nucleotide (DSSR) in a small distorted DNA complex whose geometry was obtained by an ab initio calculation. I think it might have to do with the lack of planarity.

Title: Re: base/nucleotide recognition
Post by: xiangjun on February 28, 2018, 02:27:50 pm

Could you please post a (minimal) example that illustrates the issue unambiguously?

Xiang-Jun

Title: Re: base/nucleotide recognition
Post by: cys on February 28, 2018, 02:40:29 pm

Here is a minimal example. Thanks.

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 -5.907 -5.447 -2.226 1.00 00.00 C
ATOM 182 C6 DT B 8 -7.630 -6.227 -0.557 1.00 00.00 C
END

Title: Re: base/nucleotide recognition
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

Title: Re: base/nucleotide recognition
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.

Title: Re: base/nucleotide recognition
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.

Title: Re: base/nucleotide recognition
Post by: xiangjun on February 28, 2018, 04:58:16 pm

Again, show exactly what you did so other can reproduce the problem.

Title: Re: base/nucleotide recognition
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

Title: Re: base/nucleotide recognition
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.

Title: Re: base/nucleotide recognition
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.

Title: Re: base/nucleotide recognition
Post by: xiangjun on February 28, 2018, 06:20:03 pm

Once again, reproducibility is the key, even for this presumably simple case.

Title: Re: base/nucleotide recognition
Post by: cys on February 28, 2018, 06:45:06 pm

I deleted X3DNA and reinstalled it. It's now working for this example.

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

3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: cys on February 28, 2018, 02:19:12 pm