無風的日子

1.      取得檔案  fetch 1guv
2.      選擇胺基酸 à 右下角”S”白字
3.      標示某胺基 
 select bb, name c+o+n+ca # Atoms included in the
# named-selection are indicated
# with pink dots in the viewer.
 color yellow, name c+o+n+ca # Backbone are colored yellow,
l   color blue, cys/
l   show sticks, cys/
l      show cartoons, a/10-12/ca
l     color white    # Everything turns white.  This looks fine on the  default black background,  but causes disappearance  if you've changed the background to white.
l     color orange, pept       # Remember that "pept" is our object−name,  so the entire object is colored orange.
l     color green, resi 50+54+58    # The representation of residues numbered 50, 54 and 58  is colored green.
l     color yellow, resi 60−90     # The representation of residues numbered 60 through 90 is colored yellow.
l     color blue, akeeper     # Residues which were collected in the named selection "akeeper," are colored blue.
l     color red, ss h            # The representations of  helical residues  are colored red.
l     color yellow, ss s           # The representations of beta sheet residues are colored yellow.
l     color green, ss l+""      # The representations of  loop and unassigned residues  are colored green.
4.      Secondary Structure Assignment
l   show cartoon
l   alter 11-40/, ss='H'  # assign residues 11-40 as helix
l   alter 40-52/, ss='L'   # assign residues 40-52 as loop
l   alter 52-65/, ss='S'   # assign residues 52-65 as sheet
l   rebuild            # regenerate the cartoon
5.       Cartoon Types
l   set cartoon_color,blue
l   set cartoon_cylindrical_helices,1
l   set cartoon_fancy_helices, 1
l   set cartoon_smooth_loops, 1
l   set cartoon_highlight_color, grey
l   set cartoon_transparency, 0.5
6.      高品質輸出
l   ray 2400,2400
l   file à  save image as à PNG
7.      Global Protein Surface Survey Plugin
l   place “GPSSpyMOL.py” file into the following directory: $PYMOLPATH/module/pmg_tk/startup/
l   "Plugin" menu à “Global Protein Surface Survey”.
l   "GPSS Surfaces All" shows all CASTp and ligand, metal, and peptide surfaces..
l   Enter a PDB identification code:
l   The plugin will load the PDB and all the associated surfaces. All pockets are shown in surface mode. Simply click on the surface name to toggle on/off.
8.      Hydrogen Bonding
l   distance 542/oe1,538/ne
l   distance 542/oe2,538/nh2
l   hide labels, dist01
l   label (542/oe1), " %s" % (" E542")
l   label (538/ne), " %s" % (" R538")
9.      Show Sticks ball
l   # turn on the representation for everything in PyMOL
preset.ball_and_stick('all')

l   Balls with sticks really look nice. You can even create your own style of this, with control over sphere_scale and stick_radius.
hide lines
show sticks
show spheres
set stick_radius=0.1
set sphere_scale=0.25
l   Also OK:
show sticks
set valence, on
set stick_ball, on
set stick_ball_ratio, 3
set stick_radius, 0.12



10. Movies

load test/dat/pept.pdb
# load a structure
mset 1 x60
# define the movie
util.mrock(1,60,10,1,1)
# issues mdo commands to create +/− 10 deg. rock over 60 frames


set ray_trace_frames=1
set cache_frames=0
mclear

mpng mov
# will create mov0001.png, mov0002.png, etc.