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11
Dear Dr. Xiang-Jun Lu,
I am really thankful for such a detailed reply.  It is very reassuring to know that there are "No right or wrong parameters here"  :)
I will surely report back discrepancies If I observe any in the further analysis. Thanks a lot once again.

Best Regards,
Mandar Kulkarni
12
Hi Mandar,

Quote
I am analyzing Z-DNA duplex (PDB ID: 1I0T.pdb) using 3DNA (v2.3-2017feb08) and Curves+ both. I have removed water and other molecule from PDB and only DNA coordinates are present. The input for Curves+ is generated using find_pair -c+ option.
3DNA command:
find_pair 1I0T.pdb stdout | analyze -c stdin
Curves+ command:
find_pair -c+ 1I0T.pdb curves_1I0T.inp
./Cur+ < curves_1I0T.inp
---------------
I have attached PDB file and both output files to the mail.

Thanks for providing the detailed commands you used and attaching the corresponding data files. I can reproduce your reported results from 3DNA (v2.3) and Curves+.

3DNA is working as expected for the Z-DNA structure (1I0T). For your reference, you could running the following commands:

Code: [Select]
find_pair 1I0T.pdb | analyze   # generate 1I0T.out
rebuild -atomic bp_step.par 1I0T-3dna.pdb
find_pair 1I0T-3dna.pdb | analyze   # generate 1I0T-3dna.out

Comparing the parameters in files 1I0T.out and 1I0T-3dna.out, you'd notice that they are virtually the same. See Table 3 of the 2003 3DNA NAR paper, "Root mean square deviation (in Å ) between rebuilt 3DNA models and experimental DNA structures", for A-, B-DNA, and a DNA-protein complex. Moreover, the simple relationships between step and helical parameters,  see equations 3 and 4 of the above mentioned 3DNA paper, still hold as for right-handed A- or B-DNA.

Note also that you do not need to remove water and other molecule from the PDB file for 3DNA to work.

Quote
I observed that the Shift and TIlt values for dinucleotide steps have similar values but exactly opposite signs. Also, X-displacement, Y-displacement, Inclination values are totally different (ignoring terminal base pairs) compared to 3DNA results.

This is a sharp observation. In my understanding (from the perspective of 3DNA), the opposite signs for Shift and Tilt values in Z-DNA are due to different conventions for base-pair reference frames between 3DNA and Curves+. The differences in helical parameters (X-displacement, Y-displacement, Tip, and Inclination) are a bit more complicated, but they are also directly related to the differences in base-pair reference frames. No right or wrong parameters here, just different results based on (maybe slightly) different underneath assumptions. It is up to the users to make their own choices.

In the future, it may be possible that 3DNA and Curves+ could reach an agreement on the analysis of Z-DNA structures or those with non-canonical base pairs. Since both 3DNA and Curves+ are open source, you're welcome to dig into the details of these differences and report back your findings. User-feedbacks are always welcome on the 3DNA Forum.

Hope this clarifies your confusions a bit.

Xiang-Jun
13
General discussions (Q&As) / Re: Shift and Tilt values of Z-DNA : 3DNA and Curves+
« Last post by xiangjun on April 30, 2018, 03:00:01 pm »
Dear Mandar,

Thanks for using 3DNA and for posting your questions on the Forum.

The questions on differences between 3DNA and Curves+ for Z-DNA structures have not been asked before. Given the sample files you provided, I understand what you mean. I will look into the questions carefully. Since these questions are out of 3DNA per se and technical in nature, it may take me some time to get back to you.

Best regards,

Xiang-Jun
14
General discussions (Q&As) / Shift and Tilt values of Z-DNA : 3DNA and Curves+
« Last post by mandar on April 30, 2018, 09:50:09 am »
Dear Dr. Xiang-Jun Lu,
I am analyzing Z-DNA duplex (PDB ID: 1I0T.pdb) using 3DNA (v2.3-2017feb08) and Curves+ both. I have removed water and other molecule from PDB and only DNA coordinates are present. The input for Curves+ is generated using find_pair -c+ option.
3DNA command:
find_pair 1I0T.pdb stdout | analyze -c stdin
Curves+ command:
find_pair -c+ 1I0T.pdb curves_1I0T.inp
./Cur+ < curves_1I0T.inp

I observed that the Shift and TIlt values for dinucleotide steps have similar values but exactly opposite signs. Also, X-displacement, Y-displacement, Inclination values are totally different (ignoring terminal base pairs) compared to 3DNA results.

What could be the possible reason for such difference? I have searched the forum, but I did not find any discussions related to such discrepancy. 
I have attached PDB file and both output files to the mail. Thanks in advance. I look forward to your reply.

Best Regards,
Mandar Kulkarni
15
The issues you experienced with "find_pair" have been reported many times (searching the Forum should give you some hints). The source of the missing or mis-assigned pairs is due to the irregularity of the structure under consideration. Some of the 'assumed' pairs are simply too distorted to be taken as a pair. Using your attached 'plus2.MD.traj.09.pdb' as an example, DA86 and DT587 certainly do not form a pair in any (canonical) sense -- see the attached fragment with DA86 and DT587 embedded.

In such cases, if you insist that nucleotides such as DA86 and DT587 should be taken as a pair, you can manually edit the output from "find_pair" as desired. You can think of the scenario where "find_pair" does not exist, and you have to prepare an input file with pairing info by hand.

The "analyze" program will follow strictly the pairing info as provided in the input file.

Xiang-Jun
16
Good afternoon.
I'm needing to generate ref_frame and/or .par files from a series of pdb files sent to me by a collaborator. These pdb files are from MD work (from 'ptraj'). Upon inspection of the pdb file, they lack CONECT information at the bottom and the final letter code column on the far right.

However, I have been able to generate my desired files from most of these pdb files. There are a few, however, that the number of base pairs and the number of bases do not match. I'm expecting 336 base pairs and I only get data for 335, 334, or 332. PYMOL use shows that these trajectories do not have base pairing, some bases ninety-degrees from its complement. However, my 3DNA files do not give me 672 base info, only 335*2, 334*2, or 332*2.

Here's my question: Is there a way using 3DNA that even if the bases are not bound, I should get values for them so that every 'find_pair' and 'analyze' output file is made up of 336*2 bases? I've attached two files in particular that are of frustration.
17
General discussions (Q&As) / Re: build a DNA triangle for Gromacs
« Last post by xiangjun on April 17, 2018, 11:43:22 pm »
Hi Luxuan,

Thanks for your interested in using 3DNA and for posting your questions on the 3DNA Forum. Is your DNA triangle a planar structure? Is it equilateral? What the length of each side? Are the three sides connected?

There may be tools (e.g., "AMBER NAB") that better fit your needs. 3DNA does not provide a command to directly construct such a DNA triangle. Nevertheless, 3DNA has some low-level facilities for applications like this. For examples, you could use the fiber command to build three straight helices (in B-or A-form DNA) of selected sequence. Using analyze, you can locate the positions of a regular helix. Combined with case-specific geometric operations, 3DNA may help lead to a bottom-up approach that is reproducible via a script.

Check "build dna bulges and extend dna duplex at both terminals via 3dna" and search the Forum for more applications.

Xiang-Jun
18
General discussions (Q&As) / build a DNA triangle for Gromacs
« Last post by glx55483 on April 17, 2018, 10:06:25 am »
Dear Dr. Lu,

I would like to use 3DNA to construct a DNA triangle (as shown in the attached picture) .
In the 3DNA software, can we manually input the coordinates of the central point of each DNA double helix so that they are placed in a specific position? If not, how can the double helix be translated to a specific placement? Also, can such a triangular structure be realized in 3DNA?

Thanks in advance.
Luxuan Guo
19
Thanks you Dr.!

I didn't know that update on WebStar3D site

Regards!
20
Thanks for posting a DSSR-related question on the 3DNA Forum, and for correcting the link to the CompAnnotate paper. I became aware of this work shortly after its publication, and believe it is a useful resource in RNA structural bioinformatics.

As a meta-analysis tool, CompAnnotate takes advantage of other tools (including DSSR) in the initial identification of base-pairs, as noted below:

Quote
"Annotated base-pairing lists from the existing methods (MC-Annotate, RNAView, FR3D, DSSR and ClaRNA) are used as input for CompAnnotate and the corresponding modified base-pairing lists come as output."

To better appreciate the difference between DSSR and CompAnnotate, take a look of another tool "WebSTAR3D: a web server for RNA 3D structural alignment" developed by the same group. In the WebSTAR3D paper, the authors wrote:

Quote
Before aligning structures, STAR3D preprocesses PDB files with base-pairing annotation using either MC-Annotate (Gendron et al., 2001; Lemieux and Major, 2002) (for PDB inputs) or DSSR (Lu et al., 2015) (for PDB and mmCIF inputs) and pseudo-knot removal using RemovePseudoknots (Smit et al., 2008).

It is worth noting the following update on the WebSTAR3D website (see the attached screenshot),

Quote
Update 7/11/2017: WebSTAR3D no longer employs MC-Annotate for base pairing annotation.

Further down the webpage, it is noted "Before aligning structures, WebSTAR3D preprocesses PDBs with base pairing annotation using DSSR". So now DSSR is the only choice left for base-pair annotation.

As documented in the User Manual, DSSR has many more features to offer than just identifying and annotating base pairs. In case users have any questions, the 3DNA Forum is the way to go.

Hope this clarifies some of your confusions.

Xiang-Jun
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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.