How to set up 3DNA on Windows

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Hari Seldon:
Microsoft Windows [Version 10.0.15063]

linux@DESKTOP-JS6SA18 C:\Users\linux
> echo %X3DNA%
D:\Documents\NYU\Projects\Gunsalus\Code\3DNA\x3dna-v2.3\

linux@DESKTOP-JS6SA18 C:\Users\linux
>

xiangjun:
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: ---dir %X3DNA%\bin
%X3DNA%\bin\find_pair
--- End code ---

Xiang-Jun

Hari Seldon:
Microsoft Windows [Version 10.0.15063]

linux@DESKTOP-JS6SA18 C:\Users\linux
> 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

linux@DESKTOP-JS6SA18 C:\Users\linux
> %X3DNA%\bin\find_pair
'D:\Documents\NYU\Projects\Gunsalus\Code\3DNA\x3dna-v2.3\\bin\find_pair' is not recognized as an internal or external command,
operable program or batch file.

xiangjun:
From your previous reply,

--- Code: ---> echo %X3DNA%
D:\Documents\NYU\Projects\Gunsalus\Code\3DNA\x3dna-v2.3\
--- End code ---

Now you've

--- Code: ---> 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
--- End code ---

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: --- 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
--- End code ---

Best regards,

Xiang-Jun

Hari Seldon:
I needed to re-extract x3dna-v2.3.zip because at first I just hit the extract button on the zip file then it creates D:\Documents\NYU\Projects\Gunsalus\Code\3DNA\x3dna-v2.3\x3dna-v2.3 and then I copied and pasted the x3dna-v2.3 folder into D:\Documents\NYU\Projects\Gunsalus\Code\3DNA\ to get rid of the duplicate x3dna-v2.3. That extraction and copy-paste created empty directories somehow.

What worked was not extracting at all and just entering the zip file and cut and pasting the x3dna-v2.3 folder from the zip file into D:\Documents\NYU\Projects\Gunsalus\Code\3DNA\. After that find_pair -h works (see below), however there was a strange message I got while cut and pasting

I let the files overwrite.

Microsoft Windows [Version 10.0.15063]

linux@DESKTOP-JS6SA18 C:\Users\linux
> find_pair -h
===========================================================================
NAME
find_pair - locate base-pairs and helical regions
SYNOPSIS
find_pair [OPTION] PDBFILE OUTFILE
DESCRIPTION
locate base-pairs and helical regions given a PDB data file. Its
output can be directly fed into analyze, cehs and Lavery's Curves
program.
-s, -1 treat the whole structure as a continuous single helix.
Useful for getting all backbone torsion angles
-c get Curves input for a duplex
-c+ get input for Curves+ (duplex, ATOM records only)
-d generate a separate output file for each helical region
-p find all base-pairs and higher-order base associations
-a read in only the ATOM records, ignoring HETATM records
-z more detailed base-pairing information in the output
-h this help message (any non-recognized options will do)
INPUT
PDB data file
One-letter options can be in either case, any order and combined
EXAMPLES
find_pair sample.pdb sample.inp
find_pair -p sample.pdb allbp_list
find_pair -c+ sample.pdb sample_c+.inp
[then run: Cur+ < sample_c+.inp]
OUTPUT
base-pair listing for input to analyze, cehs and Curves
bestpairs.pdb, hel_regions.pdb, col_chains.scr, col_helices.scr
allpairs.pdb, multiplets.pdb, mulbp.inp
SEE ALSO
analyze, cehs, anyhelix, ex_str, stack2img
AUTHOR
3DNA v2.3.1-2017jun24, created and maintained by Xiang-Jun Lu (PhD)

Please post questions/comments on the 3DNA Forum: http://forum.x3dna.org/
Please check 'http://x3dna.org/citations' on how to cite 3DNA --- THANKS!
===========================================================================

linux@DESKTOP-JS6SA18 C:\Users\linux
>

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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.

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