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Messages - rwmolt

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Howtos / Non-Natural Amino Acids
« on: March 23, 2017, 05:26:59 am »
The following attached PDF represents some simple pitfalls/solutions toward using 3DNA with non-natural amino acids. Via 3DNA and dox3DNA, I was able to publish an article recently in Nucleic Acids Research:

Thank you for your expertise. This is illustrative of the care that must be exercised in interpreting what this parameter means; the raw values were disturbing when interpreted in the traditional sense of what this looks like for a normal DNA helix. I appreciate your help.

Good afternoon!

I am seeing something rather anomalous in the application of 3DNA toward a given PDB structure. A sample PDB is attached that shows the oddity. If you run 3DNA, it will report an X-displacement of 69Å. It is not unique to this one PDB; I have examples ranging as high as 300Å. Obviously the x-displacement is, empirically, not 69Å for any dinucleotide step. In particular, it occurs for a non-natural nucleic acid

Other parameters look "reasonable," but I lack an independent measurement check, given that this has non-natural nucleic acids. May I ask if it is obvious to you what is amiss in 3DNA's analysis?

I am having difficulty ascertaining the criterion used to classify a dinucleotide step as A-like vs. B-like vs. TA-like. What is the specific test used by the algorithm?

I cannot seem to find this in the original 3DNA paper or on the website; I sincerely hope it's not hiding in plain site.

MD simulations / Analysis of Amber .mdcrd File
« on: February 19, 2016, 11:42:23 am »
Is there a way to analyze an Amber trajectory file (.mdcrd, in my case) using 3DNA? Other than to make a ton of PDB files from the trajectory using cpptraj, of course (ends up being a lot of "needless" I/O to make these from a trajectory and then analyze). How would one load in a parameter file to define a trajectory's atom labels?

Thank you for your time,

Howtos / Mac OSX Compilation Difficulty
« on: January 18, 2016, 11:13:02 pm »

I am currently on OSX v. 10.11.2. I followed the directions for compiling said software up to the point of sourcing my profile and encountered a difficulty. Specifically, the following commands went just fine:

tar pzxvf x3dna-v2.1-linux-64bit yada yada yada
cd x3dna_v2.1/bin
setenv X3DNA '/home/xiangjun/x3dna-v2.1'
setenv PATH '/home/xiangjun/x3dna-v2.1/bin':$PATH

I do not seem to have a .cshrc file, such that I cannot
source ~/.cshrc
without getting the error
/Users/robertmolt/.cshrc: No such file or directory.

I cannot do the next command, either, perhaps as a result:
find_pair -h

I would be appreciative of any advice that can be given to compile from this point forward. I apologize if this is an elementary Linux question.

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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.