What you will find in this page:
- Bash scripts which interact with sed and awk to parse and play with
data from either 3DNA or just pdb files. I usually keep these in my
/home/esguerra/bin directory, so that I can use them as if they were
linux commands (i.e. ls, pwd, man).
- Octave and R scripts which help understand the use of Xian-Yun Lu's
3DNA, and also for analysis of 3DNA output.
- Some tips to customize 3DNA to do exactly what you want. For
example, get a ball and stick representation combined with
Calladine-Drew's block model using CPK coloring.
- /home/esguerra/bin
get_torsions
seq_num
get_bsparam
get_steps
get_helireg
xtractNkin
avevecall
- get_helireg ==> Script
to draw cilinders around DNA/RNA helical regions in r3d format. It's
particularly useful for pymol users.
- xtractNkin
==> Make kinemage of local helical vectors in helical regions
With this script you can make a kinemage of the helical vectors which are computed
for the helical regions by 3DNA. The script separates the helical regions into new folders, analizes them through 3DNA and adds the position vector to the normalized helical vectors to get the vector representation. The script now also includes the average local helical axis. This script needs the
additional file header.kin.
- avevecall
==> Compute average helical vector from individual local helical axes
vectors. This script just calculates the average helical axes vector for a given helical
region and then makes a dat file that can be glued to a kinemage for visualization.
avevecall.m
3DNA Detailed Example found on 3DNA users guide
With this script you can just follow the detailed explanation for what 3DNA does by using octave.
localhelpar.m. Yes, yes, I know
it's long and repetitive and doesn't take input or anything like this, but this was just for fun.
You'll also need:
Standard coordinates for Guanine
Experimental coordinates for Guanine 1
Experimental coordinates for Guanine 2
Standard coordinates for Cytosine
Experimental coordinates for Cytosine 7
Experimental coordinates for Cytosine 8
Now you just need to type in your prompt:
bash-3.1$ octave localhelpar.m
- Find RMSD between step-parameter average vector for Group I and all the step-parameter vectors of the large subunit of the ribosome.
This little octave script has as its input two files which contain the
step parameters resulting from a 3DNA analysis (Group I
and 1jj2_23S.steps). Using
these files as input it calculates the RMSD between them. It then makes some
histogram graphs which require a modified version of the
histo.m script which you'll need
to have in your working folder or have it in your octave path
somewhere. The reason for the histo.m modification
was to be able to change the color of the histogram, so, now you can
easily change the color of the histogram lines.
To run this script you just need to download the linked files and type
in your prompt:
bash-3.1$ octave stepavesg1.m
You can then view the output histograms in any software of your
preference. I recommend ghostview.
Pymol control in blocview
If you use blocview, you will see that when using the -t option, it
will use pymol to produce ray traced images.
If you want to customize blocview to do the ray_tracing you want pymol
to do, then you can modify the files:
/X3DNA/config/pymol_ray.par
/X3DNA/bin/x3dna_r3d2png