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Messages - xiangjun

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1
RNA structures (DSSR) / Re: running DSSR in windows
« on: Today at 12:20:42 am »
As a followup to my previous response, I've re-compiled DSSR (and SNAP) and updated the download binaries. DSSR should now work in *native Windows* without needing msys-2.0.dll. Please have a try and report back if it works as expected.

Best regards,

Xiang-Jun

2
RNA structures (DSSR) / Re: running DSSR in windows
« on: Yesterday at 10:01:44 pm »
Hi,

Thanks for using DSSR, and for posting your question on the Forum!

I've just tried to run DSSR on Windows 7, and I can reproduce your reported error message. This error should not be there: I tested DSSR a while ago and it worked on native Windows without installing msys-2.0.dll. Obviously something has happened. I will try to get this issue resolved ASAP.

Thanks for reporting.

Xiang-Jun

3
General discussions (Q&As) / Re: HADDOCK run could not be processed
« on: November 29, 2017, 04:47:20 pm »
Thanks for your followup. However, it won't be fruitful to keep trying an unknown target. As mentioned in my previous response, you need to contact the HADDOCK developer to know exactly WHAT PDB format it needs.

At the very least, do you have any example PDB file that works with HADDOCK? I also suggested you try a DNA structure (e.g., 355d) downloaded from the RCSB PDB. The two PDB files I attached can be read without problems by Jmol/PyMOL.

Sorry, I cannot be of any further help other than what I've suggested above.

Xiang-Jun

4
General discussions (Q&As) / Re: HADDOCK run could not be processed
« on: November 29, 2017, 01:44:40 pm »
DT is a standard nucleic acid base name for T in DNA, as of PDB format v3.x (if I remember it correctly). So the error message from HADDOCK means that it is strict (picky) with its input of PDB format. As a test, you may download the DNA structure (e.g., 355d) from the RCSB PDB, and submit it to HADDOCK to see what happens.

I've re-created a new version of the PDB filedna-new2.pdb (attached) for you to try: it has T instead of DT etc.

Best regards,

Xiang-Jun


As a side note, such HADDOCK-related questions are better directed to its creators/maintainers. They know exactly what PDB format they support, and may provide you some working examples.


5
General discussions (Q&As) / Re: HADDOCK run could not be processed
« on: November 29, 2017, 12:26:31 pm »
Thanks for posting on the 3DNA Forum!

Where/how did you get the dna.pdb file you attached?

Could you please try the attached dna-new.pdb file and report back if it works?

Best regards,

Xiang-Jun

6
MD simulations / Re: Analysis of major groove and minor groove
« on: November 20, 2017, 12:00:07 pm »
In 3DNA, the algorithm for characterizing minor and major groove widths of a DNA duplex is based on the 1998 JMB paper of El Hassan and Calladine, as shown below:

Quote
Minor and major groove widths: direct P-P distances and refined P-P distances
   which take into account the directions of the sugar-phosphate backbones

   (Subtract 5.8 Angstrom from the values to take account of the vdw radii
    of the phosphate groups, and for comparison with FreeHelix and Curves.)

Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of
     Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343.

More specifically, the "Appendix: Calculation of Major- and Minor-groove Widths" which is included in the 3DNA distribution ($X3DNA/doc/groove-widths.pdf). See 3DNA v2.x source code, if you want to get to the bottom of this issue.

HTH,

Xiang-Jun

7
Quote
there is a stacking interaction between ROS and one of the adenine base in the 2D Diagram & Interactions.

http://www.rcsb.org/pdb/explore/explore.do?structureId=1f1t

My question is whether DSSR can detect such ligand and RNA interaction?

No, in general. This feature is beyong DSSR’s design scope, at least for now. Why not using the result from reported from the RCSB PDB website? It is an ‘authoritative’ resource, isn't it?

Quote
Also, generally speaking, can DSSR detect protein/peptide and nucleic acid stacking interaction? For example, the stacking between aromatic ring of Phenylalanine and nucleic acid base?

You may find SNAP helpful. Again, do not forget the many other resources/tools in the field.

Xiang-Jun

8
RNA structures (DSSR) / Re: Definition of Helix Form
« on: November 13, 2017, 02:39:09 pm »
Quote
PS. these data is under publication so I am not sure if I can provide further details but I will try my best to give you as much detain as you want.

I understand. Note also that the A-, B-, and Z-form classification algorithm implemented in DSSR is unpublished yet, as I mentioned previously. DSSR contains many undocumented features, which, if elaborated in combination with a survey of the PDB, could lead to solid publications. I've limited resources, and have to focus on the essence of DSSR as a whole. I'm glad to see that some users indeed have taken advantage of specific features of what DSSR has to offer. With collaborations, I may help to dig into some specific topics more thoroughly and efficiently.

I've no comment on your unpublished results. Since you're also using 3DNA v2.x, it helps to check the A- and B-form classification results from the analyze program. The fiber also contains the -rna option.

Xiang-Jun

9
RNA structures (DSSR) / Re: General questions of H-bond section in DSSR
« on: November 13, 2017, 02:01:21 pm »
Quote
Is there any command to parse json if we have already generated the json file?

Sure. The pipe form is just a shorthand to avoid an intermediate file. You can certainly generate the JSON file first, and then parse it using jq -- see the excellent documentation of jq for examples.

Code: Ruby
  1. x3dna-dssr -i=3bnq.pdb --get-hbond --json | jq .hbonds[1]
  2.  
  3. # can be decomposed into the following two steps:
  4. x3dna-dssr -i=3bnq.pdb --get-hbond --json -o=3bnq-hbonds.json
  5. jq .hbonds[1] 3bnq-hbonds.json
  6.  
  7. # all with the following results:
  8. {
  9.   "index": 2,
  10.   "atom1_serNum": 59,
  11.   "atom2_serNum": 975,
  12.   "donAcc_type": "standard",
  13.   "distance": 2.532,
  14.   "atom1_id": "O6@A.G3",
  15.   "atom2_id": "N4@B.C23",
  16.   "atom_pair": "O:N",
  17.   "residue_pair": "nt:nt"
  18. }
  19.  

Xiang-Jun

10
RNA structures (DSSR) / Re: General questions of H-bond section in DSSR
« 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.

11
RNA structures (DSSR) / Re: General questions of H-bond section in DSSR
« 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

12
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

13
RNA structures (DSSR) / Re: General questions of H-bond section in DSSR
« on: November 02, 2017, 11:41:55 am »
Quote
Sorry I gave a long list of questions yesterday. Here, I just post a few questions in terms of the H-bond in DSSR json.

Related questions are always welcome on the Forum. For ease of communication, just remember to keep each thread focused on a single topic, as you did here.

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?

Using the following command, with jq (v1.5), the result seems clearer.

Code: [Select]
# x3dna-dssr -i=1pfe.pdb --symm --get-hbond --json | jq .hbonds[30]

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

Quote
(1) How do I know which atom is H-bond donor and which is acceptor, like do you always put acceptor in the first place(atom1)?
(3) Wha does the 'serNum' mean here?

The list of H-bonds is ordered by atom serial numbers of the two H-bonding atoms. The atom serial number is taken from the corresponding PDB file. See the Coordinate Section, especially ATOM/HETATOM records of the documentation of the PDB format for details. The "toggle H-bonds" button in the DSSR-Jmol webpage takes advantage of this feature.

Quote
(2) If the 'donAcc_type' is questionable, what does it mean? Does it mean that DSSR probably doesn't guess the valence properly?

It simply means DSSR cannot decide this is a donor-acceptor compatible H-bond, even though it fulfills the geometric criteria. It is up to the user to decide if this H-bond is feasible.

If you provide a concrete example, I may be able to give you more details on this topic.

HTH,

Xiang-Jun

14
Feature requests / Re: Rebuild DNA structures based on 28 parameters
« on: November 02, 2017, 10:32:51 am »
Quote
As an alternative, is it possible that first I would modify the DNA structure by modifying bp_step.par file, then reanalyze the structure which will produce new bp_step.par and bp_helical.par file. In the second step, I would modify bp_helical.par file with my parameter values. This may generate the modified DNA structure with 18 modified parameters. Is this approach is correct?

Interesting idea. Please have a try and let us informed what you get.

Quote
Further Sir, I am trying my best to modify DNA backbone angles of a DNA structure separately but I am not getting any success. May you please guide me in this regard.

3DNA is of not much help here, sorry. You may try NAB (Nucleic Acid Builder), from the David Case lab at Rutgers. NAB “provides a programming environment for geometric and force-field manipulations of nucleic acids (and proteins as well).”

Xiang-Jun

15
MD simulations / Re: do_x3dna as a plugin for VMD and update in dnaMD
« on: November 01, 2017, 08:29:13 am »
Hi Rajendra,

Nice effort! Now do_x3dna and 3DNA are reaily accessible to the huge VMD user community.

Thanks for keep us informed of your new progress!

Xiang-Jun

Pages: [1] 2 3 ... 77

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.