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22
Ths link you gave is invalid. Could you fix it?

Xiang-Jun
23
Hello Dr. Xiang-Jun Lu:

This is the paper thas DSSR appears: https://academic.oup.com/nar/article/45/14/e136/3875524

I'd like to know your opinion about the DSSR performance compared with the new "CompAnnotate".

Regards. See you!
24
RNA structures (DSSR) / Re: Centre of Mass Pseudodihedral Angle
« Last post by xiangjun on April 03, 2018, 11:29:30 am »
Thanks for your followup. Now I can understand your original question a bit better. So COM stands for "center of mass" based on the attached figure caption. I still do not know what "CPD" stands for.

From the attached figure, it is still not clear to me what the two sugars above the target base are. Do the corresponding bases (attached to the sugars) must form a Watson-Crick (WC) pair? Do the three nucleotides where the base is in the middle must be consecutive in sequence?

Based on my understanding, I do not think adding this pseudo torsion angle (θ) is a good fit for DSSR (at least at this stage). See my post titled "Request for new features".

Why not ask for help from the author who defined this parameter? If that does not work out, you may write your own code or hire someone with basic programming skills for this purpose. Assuming the structure is a double helix with WC pairs, it should not be a big deal.

Xiang-Jun
25
RNA structures (DSSR) / Re: Centre of Mass Pseudodihedral Angle
« Last post by hijibijbij on April 03, 2018, 11:10:11 am »
 i am talking about COM pseudo dihedral angle, a restraint co-ordinate for doing umbrella sampling. here we restraining COM of two sugar molecule above target base, one sugar molecule below of it and the target base. For further understanding you can see the attachment.
26
RNA structures (DSSR) / Re: Centre of Mass Pseudodihedral Angle
« Last post by xiangjun on April 03, 2018, 08:33:33 am »
Hi,

Could you please let us know what exactly is “CPD (Centre of Mass Pseudodihedral Angle)”? Please also provide worked example so I can understand how to calculate it from atmoic coordinates.

Thanks,

Xiang-Jun
27
RNA structures (DSSR) / Centre of Mass Pseudodihedral Angle
« Last post by hijibijbij on April 03, 2018, 07:58:19 am »
Hi,
 
I have a silly question. I am very new in this field, I am trying to simulate a RNA structure. For that I need to measure the CPD (Centre of Mass Pseudodihedral Angle) angle of RNA. But some how I am not getting it in dssr-torsion.txt. Can anyone  please suggest how to find it or how to calculate it
Thank you in advance
28
Howtos / Re: Mac OSX Compilation Difficulty
« Last post by xiangjun on April 02, 2018, 03:43:08 pm »
Thanks for chiming in regarding 3DNA installation in tcsh shell on macOS. The more such user feedbacks, the better.

Best regards,

Xiang-Jun
29
Howtos / Re: Mac OSX Compilation Difficulty
« Last post by songzh on April 02, 2018, 03:33:47 pm »
To add the command lines in .tchsrc file, in my Mac, I just do like this:

[mwc-xxxx:~/3DNA] myname% vi ~/.tchsrc

then input the "setenv  3DNA'....." command lines. it works for me.
30
Hi Miriam,

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

I've a quick look of PDB entry 1ZRC, and found the following:

Quote
Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 2.54(1.65)

The structure as a whole is curved to fit a sensible linear helical axis, as noted in the $X3DNA/config/misc_3dna.par:

Quote
# Section 4: is this double helix curved?
#   criterion to decide if a helix is strongly curved.
#   if relatively straight, 'analyze' will output a set of
#   global parameters, the normalized axis vector, and the
#   two end points the helical axis passes through
<std_curved>0.6</std_curved>

To calculate a bending angle, you need to divide the DNA into two fragments, each relatively straight. See also FAQ How to calculate DNA bending angle?

You may also want to give Curves+ a try. It is frequently used for quantifying DNA curvature in literature.

HTH,

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.