Show Posts
1
General discussions (Q&As) / Re: install xdna on linux
« on: August 04, 2019, 05:38:43 pm »
It executes when I run the following command in the terminal I opened for installation,
sima@HP:~/x3dna-v2.4/bin$ pwd
/home/sima/x3dna-v2.4/bin
sima@HP:~/x3dna-v2.4/bin$ ./x3dna_setup
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
To install X3DNA, do as follows:
(0) download the 3DNA distribution for your operating system from URL
http://x3dna.org/
(1) tar pzxvf x3dna-v2.4-linux-64bit.tar.gz
# here for the 3DNA v2.4 distribution on 64-bit Linux
(2) cd x3dna-v2.4/bin
(3) ./x3dna_setup
to run X3DNA, you first need to do two things:
o set up the X3DNA environment variable
o add $X3DNA/bin to your command search path
for your 'bash' shell, add the following into ~/.bashrc:
--------------------------------------------------------------
export X3DNA='/home/sima/x3dna-v2.4'
export PATH='/home/sima/x3dna-v2.4/bin':$PATH
--------------------------------------------------------------
and then run: source ~/.bashrc
(4) to verify your installation, type: ./find_pair -h
you should see some command-line help message
Problems? Visit the 3DNA Forum at URL http://forum.x3dna.org/howtos/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
sima@HP:~/x3dna-v2.4/bin$ export X3DNA='/home/sima/x3dna-v2.4'
sima@HP:~/x3dna-v2.4/bin$ export PATH='/home/sima/x3dna-v2.4/bin':$PATH
sima@HP:~/x3dna-v2.4/bin$ source ~/.bashrc
sima@HP:~/x3dna-v2.4/bin$ ./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, or 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 v2.4.3-2019apr06, created and maintained by xiangjun@x3dna.org
Please post questions/comments on the 3DNA Forum: http://forum.x3dna.org/
Please check 'http://x3dna.org/citations' on how to cite 3DNA --- THANKS!
===========================================================================
sima@HP:~/x3dna-v2.4/bin$ echo $SHELL
/bin/bash
but when I close the terminal I can't call the software.
sima@HP:~$ ./find_pair -h
bash: ./find_pair: No such file or directory
sima@HP:~$ cd x3dna-v2.4/bin
sima@HP:~/x3dna-v2.4/bin$ ./find_pair -h
Please set the X3DNA environment variable
Run 'x3dna_setup', and visit http://forum.x3dna.org/ for more info.
sima@HP:~/x3dna-v2.4/bin$ pwd
/home/sima/x3dna-v2.4/bin
sima@HP:~/x3dna-v2.4/bin$ ./x3dna_setup
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
To install X3DNA, do as follows:
(0) download the 3DNA distribution for your operating system from URL
http://x3dna.org/
(1) tar pzxvf x3dna-v2.4-linux-64bit.tar.gz
# here for the 3DNA v2.4 distribution on 64-bit Linux
(2) cd x3dna-v2.4/bin
(3) ./x3dna_setup
to run X3DNA, you first need to do two things:
o set up the X3DNA environment variable
o add $X3DNA/bin to your command search path
for your 'bash' shell, add the following into ~/.bashrc:
--------------------------------------------------------------
export X3DNA='/home/sima/x3dna-v2.4'
export PATH='/home/sima/x3dna-v2.4/bin':$PATH
--------------------------------------------------------------
and then run: source ~/.bashrc
(4) to verify your installation, type: ./find_pair -h
you should see some command-line help message
Problems? Visit the 3DNA Forum at URL http://forum.x3dna.org/howtos/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
sima@HP:~/x3dna-v2.4/bin$ export X3DNA='/home/sima/x3dna-v2.4'
sima@HP:~/x3dna-v2.4/bin$ export PATH='/home/sima/x3dna-v2.4/bin':$PATH
sima@HP:~/x3dna-v2.4/bin$ source ~/.bashrc
sima@HP:~/x3dna-v2.4/bin$ ./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, or 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 v2.4.3-2019apr06, created and maintained by xiangjun@x3dna.org
Please post questions/comments on the 3DNA Forum: http://forum.x3dna.org/
Please check 'http://x3dna.org/citations' on how to cite 3DNA --- THANKS!
===========================================================================
sima@HP:~/x3dna-v2.4/bin$ echo $SHELL
/bin/bash
but when I close the terminal I can't call the software.
sima@HP:~$ ./find_pair -h
bash: ./find_pair: No such file or directory
sima@HP:~$ cd x3dna-v2.4/bin
sima@HP:~/x3dna-v2.4/bin$ ./find_pair -h
Please set the X3DNA environment variable
Run 'x3dna_setup', and visit http://forum.x3dna.org/ for more info.
