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11
RNA structures (DSSR) / Re: General questions of H-bond section in DSSR
« Last post by lvelve0901 on November 13, 2017, 10:05:22 am »
Hi Xiangjun,

Your answer is very clear and concrete. I think now I understand how 3DNA identify the H-bonds in general. I will keep posting other PDB examples in the future if we find something wired in the Hbond section since my rotation students is manually inspecting them now. Do you think we should post here or start a new topic in this forum for other PDB?

Also, I tried your way to parse json using jq and it works. But the issue by doing this


x3dna-dssr -i=3bnq.pdb --symm --get-hbond --json | jq .hbonds[1]


You will first run the DSSR and generate json file. Sometimes for a large PDB file it will take a long time. Is there any command to parse json if we have already generated the json file?

Thanks.

Best,
Honglue
12
RNA structures (DSSR) / Re: human telomeric g quadruplex - base stacking energy
« Last post by bciezah1 on November 13, 2017, 08:58:12 am »
Dear xiangjun,

I will right now. Thank you a lot!

Best wishes,

Basilio.
13
RNA structures (DSSR) / Re: General questions of H-bond section in DSSR
« Last post by xiangjun on November 12, 2017, 12:46:15 pm »
Hi Honglue,

Thanks for clarifying the Unicode issue of your Python-based JSON parser. DSSR-generated JSON output is in the ASCII charset, so Unicode is an overkill in this case. The detailed examples you provided are very helpful.

Quote
x3dna-dssr -i=3bnq.pdb --symm --get-hbond --json | jq . hbonds[1]

However, it outputs

Processing file '3bnq.pdb'
jq: error: Could not open file hbonds[1]: No such file or directory

The error is due to the extra space between the dot and hbonds[1], which makes jq to take hbonds[1] as the JSON file to process.

The following command (jq .hbonds[1]) works, as expected. Also note that no need to use the --symm option in this case.
Code: [Select]
#x3dna-dssr -i=3bnq.pdb --get-hbond --json | jq .hbonds[1]
{
  "index": 2,
  "atom1_serNum": 59,
  "atom2_serNum": 975,
  "donAcc_type": "standard",
  "distance": 2.532,
  "atom1_id": "O6@A.G3",
  "atom2_id": "N4@B.C23",
  "atom_pair": "O:N",
  "residue_pair": "nt:nt"
}

Quote
Example 1: Hbond index 117. donAcc_type acceptable.
Code: [Select]
#x3dna-dssr -i=3bnq.pdb --get-hbond --json | jq .hbonds[116]
{
  "index": 117,
  "atom1_serNum": 1426,
  "atom2_serNum": 1928,
  "donAcc_type": "acceptable",
  "distance": 2.612,
  "atom1_id": "OP2@C.G22",
  "atom2_id": "O41@C.PAR101",
  "atom_pair": "O:O",
  "residue_pair": "nt:ligand"
}

Quote
Example 2: Hbond index 113. donAcc_type standard.
Code: [Select]
#x3dna-dssr -i=3bnq.pdb --get-hbond --json | jq .hbonds[112]
{
  "index": 113,
  "atom1_serNum": 1406,
  "atom2_serNum": 1937,
  "donAcc_type": "standard",
  "distance": 2.63,
  "atom1_id": "OP2@C.C21",
  "atom2_id": "N32@C.PAR101",
  "atom_pair": "O:N",
  "residue_pair": "nt:ligand"
}

Quote
In both cases, it seems that the hydrogen bond geometry are very similar then why does the DSSR think they are different donAcc_type?

In DSSR, the donAcc_type is based on known or heuristically derived donor/acceptor properties of the two atoms in an H-bond.

In the case of H-bond #113, OP2@C.C21 is a known acceptor, and N32@C.PAR101 is judged as a donor. So this H-bond is between an acceptor and a donor, which is 'standard'.

In the case of H-bond #117, OP2@C.G22 is a known acceptor, but O41@C.PAR101 is judged as a hydroxyl group. As the 2'-hydroxyl group in RNA ribose sugar, it can be either an acceptor or a donor. So  this H-bond is classified as 'acceptable'.

Quote
Example 3: Hbond index 107. donAcc_type questionable.
Code: [Select]
#x3dna-dssr -i=3bnq.pdb --get-hbond --json | jq .hbonds[106]
{
  "index": 107,
  "atom1_serNum": 1323,
  "atom2_serNum": 1367,
  "donAcc_type": "questionable",
  "distance": 3.358,
  "atom1_id": "O4'@C.A17",
  "atom2_id": "O4'@C.G19",
  "atom_pair": "O:O",
  "residue_pair": "nt:nt"
}

Quote
In this case, the DSSR identify a hbonds between two O4' atom, but we know that for ribose, the O4' is unlikely to be protonated. Is this the reason why DSSR think the donAcc_type is questionable?

That's right. DSSR does not know (or care) the protonation state of the ribose sugars. It only knows that the O4' atoms are H-bond acceptors. Yet they are close together in 3D space and fulfill DSSR's geometric definition of an H-bond. So it is reported as a 'questionable' H-bond.

This is feature of DSSR, not a bug: it allows DSSR to detect all 3 H-bonds in C+C pairs in an i-motif, for example. In other cases, it may indicate a certain type of errors where users should pay attention to.

Since you're interested in H-bonds between nucleotides and the ligands, you could run the following command. DSSR detects three H-bonds between RNA and the PAR ligand. Are they what you’d expect? Have you tried other well-known software tools for H-bonding identification?

Code: [Select]
#x3dna-dssr -i=3bnq.pdb --get-hbond --json | jq '.hbonds[] | select(.residue_pair=="nt:ligand")'
{
  "index": 113,
  "atom1_serNum": 1406,
  "atom2_serNum": 1937,
  "donAcc_type": "standard",
  "distance": 2.63,
  "atom1_id": "OP2@C.C21",
  "atom2_id": "N32@C.PAR101",
  "atom_pair": "O:N",
  "residue_pair": "nt:ligand"
}
{
  "index": 117,
  "atom1_serNum": 1426,
  "atom2_serNum": 1928,
  "donAcc_type": "acceptable",
  "distance": 2.612,
  "atom1_id": "OP2@C.G22",
  "atom2_id": "O41@C.PAR101",
  "atom_pair": "O:O",
  "residue_pair": "nt:ligand"
}
{
  "index": 118,
  "atom1_serNum": 1438,
  "atom2_serNum": 1926,
  "donAcc_type": "acceptable",
  "distance": 2.644,
  "atom1_id": "N7@C.G22",
  "atom2_id": "O31@C.PAR101",
  "atom_pair": "N:O",
  "residue_pair": "nt:ligand"
}

Hope this clarifies your confusions about H-bonding identification in DSSR.

Xiang-Jun


PS. Please remember to be concrete in asking questions. Be generous in summarizing what you've learned for the benefit of yourself, and other viewers of a thread. Let's work together to make the Forum more informative.
14
RNA structures (DSSR) / Re: General questions of H-bond section in DSSR
« Last post by lvelve0901 on November 11, 2017, 05:54:22 pm »
Hi Xiangjun,

Sorry I have been busy with other stuff in lab but I do remember your question last time.

----------------------------------------------------------------------------------------------------------------------------------------------------------
----------------------------------------------------------------------------------------------------------------------------------------------------------
For your last question:


Quote
{u'index': 31, u'atom2_serNum': 212, u'residue_pair': u'nt:aa', u'distance': 3.09, u'atom_pair': u'N:N', u'atom2_id': u'N@2:B.ALA6', u'donAcc_type': u'standard', u'atom1_id': u'N3@2:A.DG3', u'atom1_serNum': 69}

How did you get the above output for PDB id: 1PFE? Specifically, where does the 'u' before each tag name come from?


Basically, I just load the json use my way (my own json parser) and print out the 'hbonds' section. In my python, when I load the json file (using import json module), the string format will be loaded as unicode. I think that's why those string will have the 'u'. I think that is just my python string encode issue. Here is more explanation of the unicode string (https://stackoverflow.com/questions/21808657/what-is-a-unicode-string). I also tried your way as you suggested (using jq) but I didn't make it work. Do I need to install jq in my computer? I installed jq from the website
https://stedolan.github.io/jq/ and put the file in my working folder then type.

x3dna-dssr -i=3bnq.pdb --symm --get-hbond --json | jq . hbonds[1]

However, it outputs

Processing file '3bnq.pdb'
jq: error: Could not open file hbonds[1]: No such file or directory


I don't know if I did the right way.

----------------------------------------------------------------------------------------------------------------------------------------------------------
----------------------------------------------------------------------------------------------------------------------------------------------------------
My new questions:

My new target structure is Mitochondrial Ribosomal Decoding Site (PDB ID: 3BNQ). I downloaded the PDB file (not biological assembly file) from RCSB. Then I try to generate the json file by typing:

x3dna-dssr -i=3bnq.pdb -o=3bnq.json --json --more --symm

I use my own json parser to look for the hydrogen bond between the RNA and the ligand PAR.

There are three examples with different don_Acc type here. All the hydrogen bonds mentioned below are labeled in the 3bnq.pse. Measure01 is the first example. Measure02 is the second example. Measure03 is the third example.

Example 1: Hbond index 117. donAcc_type acceptable.
{u'index': 117, u'atom2_serNum': 1928, u'residue_pair': u'nt:ligand', u'distance': 2.612, u'atom_pair': u'O:O', u'atom2_id': u'O41@C.PAR101', u'donAcc_type': u'acceptable', u'atom1_id': u'OP2@C.G22', u'atom1_serNum': 1426}

This is a hydrogen bond between a hydroxyl group in the ligand PAR and the OP2 atom in rG22.

Example 2: Hbond index 113. donAcc_type standard.
{u'index': 113, u'atom2_serNum': 1937, u'residue_pair': u'nt:ligand', u'distance': 2.63, u'atom_pair': u'O:N', u'atom2_id': u'N32@C.PAR101', u'donAcc_type': u'standard', u'atom1_id': u'OP2@C.C21', u'atom1_serNum': 1406}

This is a hydrogen bond between a amino group in the ligand PAR and the OP2 atom in rC21.

In both cases, it seems that the hydrogen bond geometry are very similar then why does the DSSR think they are different donAcc_type?

Example 3: Hbond index 107. donAcc_type questionable.
{u'index': 107, u'atom2_serNum': 1367, u'residue_pair': u'nt:nt', u'distance': 3.358, u'atom_pair': u'O:O', u'atom2_id': u"O4'@C.G19", u'donAcc_type': u'questionable', u'atom1_id': u"O4'@C.A17", u'atom1_serNum': 1323}

In this case, the DSSR identify a hbonds between two O4' atom, but we know that for ribose, the O4' is unlikely to be protonated. Is this the reason why DSSR think the donAcc_type is questionable?

I really appreciate your help.

Best,
Honglue


15
RNA structures (DSSR) / Re: General questions of H-bond section in DSSR
« Last post by xiangjun on November 10, 2017, 11:04:23 pm »
Could you please respond to my queries in answering your previous questions?

For your new questions, could you please post concrete examples to illustrate unambiguously what you mean? This is helpful not only for me and others to better understand you but also clarifies your own thought.

This Forum works best in a bidirectional conversation style instead of one-way Q&As.

Best regards,

Xiang-Jun
16
RNA structures (DSSR) / Re: General questions of H-bond section in DSSR
« Last post by lvelve0901 on November 10, 2017, 10:35:42 pm »
Hi Xiangjun,

I have follow up questions in terms of donAcc_type in H-bond.

Here I attach the json output file of PDB 3BNQ. In the H-bond section, I see there are three types of donAcc_type: standard, acceptable and questionable. You have already explained to me what questionable mean but could you please explain the difference between standard and acceptable?

Also, is there anyway to tell which atom is donor and which atom is acceptor?

Thank you.

Best,
Honglue
17
MD simulations / Re: about "curavture" and "tangent" in dnaMD
« Last post by Rajendra Kumar on November 08, 2017, 12:02:40 pm »
Hi,

As written in tutorial (http://do-x3dna.readthedocs.io/en/latest/notebooks/helical_axis_tutorial.html), axis coordinate is determined using two base-pairs (one base-step) by 3DNA. Therefore, number of helical-axis coordinates is less than one of total number of base-pairs.

Unit of helical-axis is A, therefore, curvature unit is (1/A). Tangents are a list of vectors with same as helical-axis unit.

With regards,
Rajendra
18
MD simulations / about "curavture" and "tangent" in dnaMD
« Last post by xroxzero on November 08, 2017, 11:14:05 am »
Hello,

I have a question about the unit of "curavture" and "tangent" in dnaMD. 

In dnaMD, my dna contains 24bp, and I type " dnaMD vsTime -i 24bp_dna.h5 -tbp 24 -bs 1 -be 24 -p "curvature" -mm sum -o curvature.dat ".

An error occur, "The requested end bp 24 is out side of 1-23 range" , why the range is 1-23?

This error occur on "tangent" ,too.

Also,I concern the unit of "curavture" and "tangent" ?



Thank you very much for your help,
Anderson
19
RNA structures (DSSR) / Re: human telomeric g quadruplex - base stacking energy
« Last post by xiangjun on November 08, 2017, 11:01:14 am »
Hi Basilio,

Try the latest DSSR v1.7.1-2017nov01 which has a section does just that. See below for an example (1xav).

Code: [Select]
List of 1 G4-stem
  Note: a G4-stem is defined as a G4-helix with backbone connectivity.
        Bulges are also allowed along each of the four strands.
  stem#1[#1] layers=3 loops=3 INTRA-molecular parallel
   1 syn=---- WC-->Major area=11.75 rise=3.73 twist=30.20 nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17
   2 syn=---- WC-->Major area=17.06 rise=3.74 twist=23.28 nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
   3 syn=---- WC-->Major                                  nts=4 GGGG A.DG6,A.DG10,A.DG15,A.DG19
    strand#1  +1 DNA syn=--- nts=3 GGG A.DG4,A.DG5,A.DG6
    strand#2  +1 DNA syn=--- nts=3 GGG A.DG8,A.DG9,A.DG10
    strand#3  +1 DNA syn=--- nts=3 GGG A.DG13,A.DG14,A.DG15
    strand#4  +1 DNA syn=--- nts=3 GGG A.DG17,A.DG18,A.DG19
    loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT7
    loop#2 type=propeller strands=[#2,#3] nts=2 TA A.DT11,A.DA12
    loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT16

Note that the identification and characterization of G-quadruplexes is a new feature of DSSR from v1.7.0. I welcome user feedback, as always.

Xiang-Jun
20
RNA structures (DSSR) / human telomeric g quadruplex - base stacking energy
« Last post by bciezah1 on November 08, 2017, 10:44:13 am »
Dear Xiang-Jun,


I wonder if 3DNA has an option to calculate the base pair stacking energy (projected area) for g-quadruplex RNA. I know 3DNA can do it for a dsDNA, but I wonder if there is the same option for g-quadruplex.

Thanks you,

Basilio.
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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.