3DNA Forum

Miscellaneous items => Users' contributions => Topic started by: mauricio esguerra on August 16, 2007, 12:58:11 am

Netiquette · Download · News · Gallery · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · Video Overview · DSSR v2.5.0 (DSSR Manual) · Homepage

Title: Script to render helical regions as cylindersr
Post by: mauricio esguerra on August 16, 2007, 12:58:11 am

Hello,

I've made a bash script to make my life easier when creating Raster 3D (r3d) files with a cylindrical representation of the straight helical regions found by 3DNA. The script can be found at:

http://eden.rutgers.edu/~esguerra/RNA/scripts.html (http://eden.rutgers.edu/~esguerra/RNA/scripts.html)

The script creates a folder named helical where it will output the r3d file.
The script works only for linux and it needs for 3DNA, raster3D and molscript to be installed.The user only has to put the script in her/his local bin directory, say:

bash> cp gethelireg /home/esguerra/bin

and then the script can be invoked from any folder where one has a pdb file.

bash>gethelireg
Type the name of your pdbfile
1kh6.pdb

Then you just chage directory to helical and you'll find the file 1kh6.pdb.r3d
The script also runs 3DNA's find_pair and analyze automatically using the default arguments of  find_pair and you can find the results in the same folder where you have your pdb coordinates file.

Now, you can just do:

pymol 1kh6.pdb.r3d

And play with the image all you want.

You can get an image like the following using ray_trace_mode in pymol:
(http://http://eden.rutgers.edu/~esguerra/CHEMISTRY/1kh6.png)



Enjoy,

Code: [Select]

#!/bin/bash
# Script to get the helical region files poc_haxis.r3d
# rename them and get them into one single file to be merged with
# the whole skeleton.
echo "Type the name of your pdb file"
read -e INPUT
#find_pair -t  $INPUT stdout | analyze
find_pair  $INPUT stdout | analyze
NUMHEL=`grep "Section #" hel_regions.pdb | tail -n 1 | awk '{print substr($3,2)}'`

mkdir helical
cp $INPUT helical/
cd helical

i="1"
while [ $i -le $NUMHEL ]
do
    echo "$i"
    mkdir rna$i.dir
    ex_str -$i ../hel_regions.pdb rna$i.dir/rna$i.pdb
    cd rna$i.dir
#    find_pair -t rna$i.pdb rna$i.inp
    find_pair rna$i.pdb rna$i.inp
    analyze rna$i.inp
    mv poc_haxis.r3d rna$i.r3d
    cp rna$i.r3d ../
    cd ..
    i=`expr $i + 1`
done
rm -rf rna*.dir
blocview -o $INPUT
echo -e "8 n  17.  0.6       -1.0 -1.0 -1.0     0.4   0 0 0 0" > translucent.r3d
cat t.r3d translucent.r3d rna*.r3d > $INPUT.r3d


Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University