Files
for running RasMol scriptsFiles
for running RasMol scriptsThese files are used to run a script, "motifs.txt", which is an
extended tour of many different DNA-binding motifs. This script is a
so-called "master script", in that it calls in turn a number of other
scripts. These scripts are listed in section 2. See the notes at the
end of that section.
These scripts also use a number of other files; some are PDB files,
with *.pdb names, and others are scripts that do various operations
such as rotating the image, with *.spt, *.scr, or *.txt names. These
are listed in section 3.
If you want to download the individual files (e.g., if you
can't make method (2a) work), links to each of them follow. In both
Netscape and Internet explorer, the files open. Click on File/SaveAs,
and save it in your "motifs" folder.
motifs.txt The master script itself. In
turn, it uses the following scripts:
gr1.txt Introductory material on DNA-binding
proteins, using glucocorticoid receptor
hth1.txt Helix-turn-helix motif, using lambda
repressor as an example
gcn4.txt Leucine zipper, using yeast GCN4 as
an example
myoD.txt Helix-loop-helix motif, using MyoD as
an example
zif268.txt 2Cys-2His zinc finger, using
Zif268
gr2.txt 4Cys zinc finger, using glucocorticoid
receptor
gal4.txt 6Cys-2Zn zinc finger, using GAL4
arc.txt beta-strand motif, using phage P22
Arc
Note: You can run any of these scripts using RasMol. To run gr1.txt, for example, enter at the command linescript "gr1.txt"For any other script, substitute its name for 'gr1.txt'.
Note: If you have trouble downloading these files, please tell me (jlittle@u.arizona.edu).
1glu.pdb glucocorticoid
receptor:DNA complex
1lmb.pdb lambda CI repressor:DNA
complex
gcn4.pdb Complex between DNA and
the bZIP portion of GCN4
myoD.pdb Complex between DNA and
MyoD
zif268.pdb Complex between DNA
and Zif268
gal4.pdb Complex between
DNA and GAL4 DNA-binding domain
arc.pdb Complex between DNA and Arc
protein
Miscellaneous scripts:
Script to look at the nucleosome is nuc2.txt . To view it you need the PDB file for the nucleosome; be sure when you run the script that both these files are in the same folder as the RasMol program. Note this script isn't completed; it just ends.
Often in writing scripts you want to have some kind of smooth movement, such as rotating the molecules. To rotate, for instance, files like x90-2.scr above tell the program to rotate it 2 degrees, wait a short period of time, rotate it 2 degrees, etc. Unfortunately, RasMol doesn't have a mechanism for telling it to wait a fixed length of time; the work-around is to give a command that takes a certain amount of time to carry out, such as redraw the screen x times. The drawback to this is that different computers take variable lengths of time to do so, and so the rotations can be too fast on fast computers and too slow on slow ones. To deal with this to some extent, I have written two sets of the rotation scripts, fast ones and slow ones. The slow ones are given above. Links to both sets are in the table below. I suggest that if you find these too slow on your computer, you download the fast ones. Put them into a separate folder (such as "motifs/fast rotations") so you will have them; then, you can copy (not move) them into the "motifs" folder, replacing the "slow" ones, and see if that works better. If your computer really screams and the slow ones are too fast, you can try editing the rotation scripts and add more lines like "script delay1.scr" between each rotation.
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If you have a fast computer and want to use the "contacts.txt" script used in class on 10/6/03, try contacts--slow.txt (which also needs delay2.scr) or even contacts--veryslow.txt .
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