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Messages - mlowe

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w3DNA -- web interface to 3DNA / Composite
« on: June 24, 2020, 05:57:46 pm »
I am trying the composite feature of web 3DNA 2.0. I would like to use my own "template PDB." However the form appears to be searching rcsb.org. Is there a way to enter my own PDB?

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General discussions (Q&As) / Re: Setting up 3D-DART with X3DNA
« on: June 06, 2020, 08:34:18 am »
I have successfully been able to run a standalone version of 3D-DART and example files. However, the instructions for using 3D-DART for custom structures cannot be found. Can 3DNA bend the DNA at places and angles that I designate? Do you have instructions? If 3DNA cannot bend the DNA, are you aware of software packages that can?

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General discussions (Q&As) / Setting up 3D-DART with X3DNA
« on: May 28, 2020, 12:21:38 am »
On a Mac, I am trying to install 3D-DART, which uses X3DNA. However the installation failed. The output and error messages are shown in the attachment. It's possible that 3D-DART was designed to use X3DNA v. 1.5. Using the current version of X3DNA (3DNA v2.4.4-2019sep09), this is what I see:

The problems seem to develop when 3D-DART tries to run the plugin X3DNAanalyze.

I noticed that my subdirectories are different from the ones listed on the 3D-DART website, which says that I should see:
BASEPARS FIBER    bin

However after installing 3DNA, I have these directories:
config     fiber    bin

The files in BASEPARS appear to be in config.
The files in FIBER appear to be in fiber.
The files in bin are still in bin.

In addition, based on looking for a similar issue on the web, it is possible that EnergyPDN.exe will not run correctly.
Any suggestions?

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.