Rasmol Tips and Tricks

Overall strategy: 
Select something
Do something to the selection

Selection commands:
select all
select his   (selects all the histidines)
select 1      (selects the first residue)
select 1,34,87
select 1-21 
select hetero    (all the hetero atoms)
select hoh         (the waters)
select hetero and not hoh   (all the hetero atoms that are not water)
select *CA    (all the alpha carbons)
C  carbonyl carbons
O  carbonyl oxygens
N  amide nitrogens
select 18 and *.CA   (select the Calpha atome of residue 18)

select sidechain
select backbone
select 18 and sidechain
select helix
select sheet
select not (helix or sheet)

Do something to it:
wireframe on 
wireframe off
wireframe 75  (makes a fatter wire - this is like the sticks command)

ribbons on
cpk  (this is spacefilling - like a cpk model)

color stuff
color red  (or blue, green, cyan, etc)
color [100,100,100]  (this gives the color is red green blue - 100,100,100 is dark grey)
color cpk  (give cpk colors)


zap (erases EVERYTHING -- YOU HAVE TO START COMPLETELY OVER...)
background white (gives a white background instead of black)

load pdb "proteins/1HRC.pdb"
script <filename>.scr   or   <filename>.txt
write <filename>.scr    (writes a script to make the view on the screen, you cannot edit this       
                                        later!) 

rotate x 10
rotate y -10
rotate z 30
translate x 10
translate y -10

Comment:
To put a comment into your script use the pound symbol: #
# This is a comment, it won't be executed

color green    #the "color green" will be executed but this comment won't!

Use comments to "morph" one script into another.  Eventually you get all your known commands into one big script and you can pick and choose what to do!

Example:
Select backbone and 1-20
#wireframe
ribbons
# wireframe 75
#color red
#color [100,100,0]
color blue

Select everything within 10 angstroms of amino acid 48
select within (10, 48)

You can also define a group of atoms or residues:
define ncac (*.N, *.CA, *.C)
This is a different definition of backbone atoms that is useful when looing at NMR structures because it does not select the amide or alpha protons. 

You use it like this:
select ncac
wireframe ncac
and etc.

You can also define a group of residues:
define helix1 (1-15)
select helix1
wireframe 75
color red

If you named all the helices, helixX X=1-5 then you can easily change their properties and colors.