Computer Modeling of Biomolecules
Presented by
Kam Bo Wong
Department of Biochemistry & Molecular Biotechnology Programme
email: kbwong@cuhk.edu.hk
http://smart.bch.cuhk.edu.hk/kbwong/index.htm
9. A DNA binding protein - GAL4 transcription factor
9.1 Load "gal4.pdb"
9.2 Change to "Cartoons" Display for protein atoms only
RasMol>
select protein
RasMol>
wireframe off
RasMol>
cartoons on
· notice that no change in display mode
was applied to the DNA molecule.
9.3 More advanced selection techniques
Try the following commands:
RasMol>
select protein
RasMol>
color white
RasMol>
select dna
RasMol>
spacefill on
RasMol>
select dna and backbone
RasMol>
color red
RasMol>
select dna and not backbone
RasMol>
color yellow
If you can still follow the syntax, try the following even more advanced
selections:
· Selection of A:T pairs of DNA
RasMol>
select (a or t) and not backbone
RasMol>
color violet
· Selection of all atoms in chain B
RasMol>
select *:B
RasMol>
color blue
· Selection of residues 1-40 of chain B
RasMol>
select 1-40:B
RasMol>
color green
· Selection of protein atoms that are within 5.0 Angstroms from DNA
RasMol>
select within ( 5.0 , dna ) and protein
RasMol>
color cyan
