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21
Feature requests / Re: Rebuild DNA structures based on 28 parameters
« Last post by Akhilesh Mishra on November 06, 2017, 09:06:39 am »
Respected Sir,
                     Is it possible to modify the rebuild code in such a manner that it starts to consider one ".par" file considering 18 parameters at once instead of two ".par" file (bp_step.par & bp_helical.par file) considering 12 parameters each?

Further Sir, I read the NAB manual but I do not get any clue that, "How could I change the backbone angle with my parameter values?" It might be, I am not focusing at right place may you please guide me to the place from where I can start.
                                   Thank You!!
22
RNA structures (DSSR) / Re: General questions of H-bond section in DSSR
« Last post by xiangjun 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
23
Feature requests / Re: Rebuild DNA structures based on 28 parameters
« Last post by xiangjun 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
24
RNA structures (DSSR) / General questions of H-bond section in DSSR
« Last post by lvelve0901 on November 01, 2017, 11:37:03 am »
Hi Xiangjun,

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.

For the H-bond between protein/peptide/ligand to nucleic acid, my target structure is 1PFE, which is a DNA bound to an antibiotic, echinomycin. I downloaded the biological assembly file and used the following command:

x3dna-dssr -i=1PFE.pdb -o=1PFE.json --json --more --symm

In the "hbonds" session of the output json file, I did found the all the DNA-drug interactions. For example,

{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}

However, I have a few questions in terms of the hbonds output.

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

Here, I attached all my files.

Thank you.

Best,
Honglue
25
Feature requests / Re: Rebuild DNA structures based on 28 parameters
« Last post by Akhilesh Mishra on November 01, 2017, 09:03:45 am »
Thank You, Sir!!

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?

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.
                 Thanks Again!! 

 
26
MD simulations / Re: do_x3dna as a plugin for VMD and update in dnaMD
« Last post by xiangjun 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
27
MD simulations / Re: local helical axis vector for strongly bent DNA
« Last post by Rajendra Kumar on November 01, 2017, 06:41:45 am »
Hello,

I would like to point out that do_x3dna contains -ref option, which executes find_pair for only first frame, and same base-pairs information is used for whole trajectory. It is written in this link: http://do-x3dna.readthedocs.io/en/latest/do_x3dna_usage.html#ref.

With best regards,
Rajendra
28
MD simulations / do_x3dna as a plugin for VMD and update in dnaMD
« Last post by Rajendra Kumar on November 01, 2017, 06:16:55 am »
Hello,

I have developed do_x3dna as a plugin for VMD (http://do-x3dna.readthedocs.io/en/latest/vmd_plugin.html). Now, two variants of do_x3dna are available, one for GROMACS and other as a plugin for VMD.

Now dnaMD can be used as both Python module (http://do-x3dna.readthedocs.io/en/latest/api_summary.html)) and command line tools (http://do-x3dna.readthedocs.io/en/latest/dnaMD_usage.html). I am still expanding the dnaMD command. dnaMD can be installed easily through pip (http://do-x3dna.readthedocs.io/en/latest/install_dnaMD.html).

With best regards,
Rajendra
29
RNA structures (DSSR) / Re: Can DSSR detect nucleic acid ligand interaction
« Last post by xiangjun on October 31, 2017, 11:29:22 pm »
Hi Honglue,

This is a long list of questions, some of which are quite general. To proceed, please start a new thread for each related topic, illustrated with concrete examples.

As you know, some of DSSR features (like the --metal option) are experimental, and not documented yet. So you may be better off trying some other more polished (and published) tools/resources. For metal interactions with nucleic acids, for example, a quick online search immediately led to the following two papers:


For H-bonding detection, you may better try the well-established and published tools: HBPlus and HBexplore, as mentioned several times already.

Xiang-Jun
30
RNA structures (DSSR) / Re: Can DSSR detect nucleic acid ligand interaction
« Last post by lvelve0901 on October 31, 2017, 10:40:31 pm »
Hi Xiangjun,

First, I want to apologize for not getting the feedback to you in time, though I carefully benchmarked the calculation as you suggested.

1. H-bond
For the H-bond between protein/peptide/ligand to nucleic acid, my target structure is 1PFE, which is a DNA bound to an antibiotic, echinomycin. I downloaded the biological assembly file and used the following command:

x3dna-dssr -i=1PFE.pdb -o=1PFE.json --json --more --symm

In the "hbonds" session of the output json file, I did found the all the DNA-drug interactions. For example,

{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}

I have a few questions in terms of the hbonds output.

(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)?
(2) If the 'donAcc_type' is questionable, what does it mean? Does it mean that DSSR probably doesn't guess the valence properly?
(3) Generally speaking, for a random ligand (not peptide-linking or DNA/RNA-linking), how does DSSR guess the valence, like how to guess which heavy atom should be bonded to hydrogen?
(4) Wha does the 'serNum' mean here?

I am training a rotation student to use DSSR to parse all the drug and nucleic acid interactions from the entire PDB so hopefully we will keep updating the issues of DSSR hbonds under the same page.

--------------------------------------------------------------------------------

2. metal

I got a bit confused about your metal sessions in the json file.

My target structure is 1HR2. It is a P4P6 domain which has many Mg2+ in the coordinates.

I again downloaded the biological assembly file and tried to type:

x3dna-dssr -i=1HR2.pdb -o=1HR2.json --json --more --symm --metal

In the output json file, there is indeed a session called 'metals'. For example,

{u'index': 3, u'ligands_long': u'', u'num_ligands': 0, u'symbol': u'Mg', u'ligands_short': u'', u'id': u'A.MG55'}
{u'index': 4, u'ligands_long': u'A.A248,A.U249,A.G250', u'num_ligands': 3, u'symbol': u'Mg', u'ligands_short': u'AUG', u'id': u'A.MG57'}

In the index 3, I assume it means there is no residue/ligand interact with MG55 right? However, if you open the PDB file, don't you think that MG55 is very closed to the cytosine 255? I guess I might misunderstand something, so my questions in terms of metals are.

(1) How does DSSR define the interactions with metal involved?
(2) More generally, how doesn't DSSR define a metal. For example,

In the structure 1D8X, the COBALT HEXAMMINE(III) (NCO) which is a metal complex is considered as metal in DSSR.
In the structure 3MGV, the VANADATE ION (VO4) which is already an negative charged ion is considered as metal in DSSR.

Is there any list which DSSR think certain atom belongs to metal category?

--------------------------------------------------------------------------------

Again, I really appreciate your help with my research all the time and really hope DSSR will be better and better.

Thanks again.

Best,
Honglue
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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.