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Messages - xiangjun

Pages: [1] 2 3 ... 74
2
RNA structures (DSSR) / Re: Quantifying base stacking interactions
« on: August 17, 2017, 03:30:03 pm »
Hi Betty,

Quote
If I were to quantify the amount of base stacking interactions by using the numbers in and out of parentheses, would the units just be Angstroms^2?

Yes, the unit is in Å2. The numbers outside () take consideration of the exocyclic atoms, while those within () use only the 6- (pyrimidines) or 9- (purines) membered base rings (polygons). You may use a Jmol/PyMOL or other molecular viewer to see how the numbers match intuitive observations.

Quote
And would you define these numbers as area of overlap of the bases?

Yes. The reported area is the overlapped polygon of the two corresponding rings projected onto the mean plane of the base normals.

Here is the relevant portion excerpt from the 2003 3DNA NAR paper:

Quote
The stacking interactions are quantified in 3DNA by the shared overlap area, in Å2, of closely associated base rings, i.e. the nine-membered ring of a purine R (A or G) and the six- membered ring of a pyrimidine Y (C, T or U), projected in the mean base pair plane. ... To account for the stacking interactions (overlap areas) of exocyclic atoms over base rings, ... an extended polygon, which includes exocyclic atoms, is used. For cytosine, the extended polygon is defined by the C1'-O2-N3-N4-C5-C6-C1' atomic sequence.

HTH,

Xiang-Jun

3
Hi Ignacio,

I'm glad to know that you've been able to "extract the groove values by running Curves+". As noted in my blogpost "Curves+ vs 3DNA", Curves+ has unique features and is more complete in its calculation of groove parameters (depths and widths). It's a good idea to always give it a try even if 3DNA also works.

As far as 3DNA is concerned, the DNA structure in PDB entry 4xrs is highly deformed. The helical fragment automatically identified by 'find_pair' in such a case is not as desired. With missing phosphate groups between neighboring pairs, the  'analyze' program can no longer calculate groove widths. In this case, you could manually edit the output from 'find_pair'  before feeding into  'analyze' to get the desired results. Imagine the scenario where you do not have access to 'find_pair' and have to prepare an input to 'analyze' manually, as you did for Curves+.

Best regards,

Xiang-Jun

4
Thanks for updating the test_modified.pdb file. Now I can see that the methylation is on atom N6 of A16. By design, 3DNA only includes the first layer of exocyclic base atoms for stacking interactions. That explains why you did not see any difference in the two output files on test_modified.pdb and test_modified_nomethyl.pdb, i.e., the methyl carbon is not considered for the calculation of overlap area.

For the record, here is the abbreviated portion from the 2003 3DNA NAR paper:

Quote
The stacking interactions are quantified in 3DNA by the shared overlap area, in A2, of closely associated base rings, i.e. the nine-membered ring of a purine R (A or G) and the six- membered ring of a pyrimidine Y (C, T or U), projected in the mean base pair plane. ... To account for the stacking interactions (overlap areas) of exocyclic atoms over base rings, ... an extended polygon, which includes exocyclic atoms, is used. For cytosine, the extended polygon is defined by the C1'-O2-N3-N4-C5-C6-C1' atomic sequence.

Sorry, 3DNA cannot be helpful in this case. You may try programs that calculate "Solvent Accessible Surface Area".

Xiang-Jun


5
Hi Atul,

Thanks for using 3DNA and for posting such a clearly defined question!

Your two attachments are identical: specifically, test_modified.pdb does not have a methyl group on A16. Could you please verify, and re-attach an updated file with a methyl-modified A16?

Best regards,

Xiang-Jun

6
General discussions (Q&As) / Re: DNA FORM A/B
« on: July 21, 2017, 02:48:02 pm »
Hi Basilio,

It means not A-, or B-, or TA-like, based on the criteria used in 3DNA. See the source code ana_fncs.c/print_PP() for details. Bear in mind that DNA has more conformational flexibility than the three types can cover.

HTH,

Xiang-Jun

7
Programs / Re: mutate_bases
« on: July 18, 2017, 05:23:23 pm »
Dest the list contain a nucleotide with chain id 'D' and residue number of '2', as you originally specified?

Quote
> mutate_bases "c=D s=2 m=U" 4jvh_250749_RNA.pdb 4jvh_250749_RNA_mut.pdb
Mutation entry 1 D:...2@:[@@@] has no PDB residue match
   1    D:...2@:[@@@]    ===> [  U.U]   residue to be mutated not in the PDB file
    Number of mutations: 0

Now does the above message make sense to you? As a new user of the program, what would you suggest to make the message clearer?

8
Programs / Re: mutate_bases
« on: July 18, 2017, 05:06:19 pm »
Just follow the example. Report back how it goes.

9
Programs / Re: mutate_bases
« on: July 18, 2017, 07:44:24 am »
Did you read the diagnostic message? The -e option may help.


10
Programs / Re: mutate_bases
« on: July 17, 2017, 06:49:07 pm »
It is a Windows peculiar again!

Try replacing single quote with double quote in the mutate_bases command again, and it should work. I've just tested the following example.
> mutate_bases 'c=a s=2 m=DA' 355d.pdb 355d_G2A.pdb
REM as you saw ... print the command-line help message

REM -- the following command works as expected
> mutate_bases "c=a s=2 m=DA" 355d.pdb 355d_G2A.pdb
   1    A:...2@:[@@@]    ===> [ DA.A]   ---done---
    Number of mutations: 1

Time used: 00:00:00:00

Since double quote also work in Linux/Mac OS, I'm refining the help message to use double quotes instead of single quotes.

Thanks for using 3DNA on Windows.

Xiang-Jun

11
General discussions (Q&As) / Re: global DNA curvature analysis
« on: July 17, 2017, 06:38:33 pm »
Hi Basilio,

I'm surprised to know that Yale is still holding a version of the 3DNA v1.5 User Manual I wrote well more than ten years ago.

The Pouderoyen et al.publication referred to there is about 1tc3, which contains a A-B junction. See also the paper "A-form conformational motifs in ligand-bound DNA structures" where 1tc3 is analyzed from a different perspective.

HTH,

Xiang-Jun

12
FAQs / Re: How to set up 3DNA on Windows
« on: July 15, 2017, 07:46:19 pm »
Glad to see things work out. The repeated folder name, ...\x3dna-v2.3\x3dna-v2.3, was due to the following two factors:

  • When x3dna-v2.3.zip is extracted, the \x3dna-v2.3 folder is automatically appended.
  • The "Extract All..." command, showing up when right-click on x3dna-v2.3.zip, will set the default folder with \x3dna-v2.3 at its last element: e.g., C:\Users\xiangjun\Downloads\x3dna-v2.3, as in my case.

I noticed this caveat while testing, but before finishing the FAQ entry. You were quick in following the original unpolished content... I've thereafter added a note to remind users to removing the \x3dna-v2.3 portion from the "Extract All..." default setting.

The double \x3dna-v2.3 folder name is actually not a big deal (just looking ugly), once one knows it -- the X3DNA environment variable simply needs to be adjusted accordingly.

Instead of right-click on x3dna-v2.3.zip and then ""Extract All...", one can simply double-click x3dna-v2.3.zip. This will create a \x3dna-v2.3 folder on par with the x3dna-v2.3.zip file. Then one can drag-and-drop the resultant \x3dna-v2.3 folder to a desired location.

Also, the X3DNA environment variable can be set directly in ConEmu terminal. And the PATH can be updated via command line as well. Once one knows the basics, the setting up process can be performed in numerous ways, and be finished in no more than a few minutes.

Xiang-Jun


13
FAQs / Re: How to set up 3DNA on Windows
« on: July 15, 2017, 01:40:49 pm »
From your previous reply,

Code: [Select]
> echo %X3DNA%
D:\Documents\NYU\Projects\Gunsalus\Code\3DNA\x3dna-v2.3\

Now you've

Code: [Select]
> dir %X3DNA%\bin
 Volume in drive D is DATA
 Volume Serial Number is 1A46-D28D

 Directory of D:\Documents\NYU\Projects\Gunsalus\Code\3DNA\x3dna-v2.3\bin

06/24/2017  11:47 AM    <DIR>          .
06/24/2017  11:47 AM    <DIR>          ..
               0 File(s)              0 bytes
               2 Dir(s)  395,301,408,768 bytes free

This is UNEXPECTED -- "0 File(s)" within %X3DNA%\bin.

The dir %X3DNA%\bin command should list the 3DNA executable files in directory "D:\Documents\NYU\Projects\Gunsalus\Code\3DNA\x3dna-v2.3\bin", as shown below in my case.


Could you do the following, to make sure you have 3DNA installed in the folder:

Code: [Select]
    REM this command should change you to the 3DNA directory --- this is a REMark (comment line)
cd %X3DNA%

    REM this command lists the content of the folder (%X3DNA%)
dir

    REM this command lists content of the examples folder within 3DNA
dir examples

Best regards,

Xiang-Jun




14
FAQs / Re: How to set up 3DNA on Windows
« on: July 14, 2017, 09:56:56 pm »
The X3DNA environment variable looks right. The problem could be due to missing the %X3DNA%\bin folder in PATH.

To verify, what the output from running the following commands (in ConEmu terminal):

Code: [Select]
dir %X3DNA%\bin
%X3DNA%\bin\find_pair

Xiang-Jun

15
FAQs / Re: How to set up 3DNA on Windows
« on: July 14, 2017, 08:30:59 pm »
Thanks for the detailed screenshots. It is weird. Things should not be that hard. Let's work together to sort things out.

Could you please do the following:

  • Within ConEmu terminal, type: echo %X3DNA%
  • On my case, the output is: C:\Users\xiangjun\x3dna-v2.3\, as originally set.

What's your output?

Xiang-Jun

Pages: [1] 2 3 ... 74

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.