| Jul 1 2004 |
buildpep "ACDF" # tetrapeptide # zoom out and create a small remote view v1=View() # the 1st view # zoom in and rotate v2=View() # the last view for i=1,100 set view View(v1,v2,i*0.01) # interpolation endforNow you can add a specific display ( cpk, skin or anything else) and add the write image command after set view . The following script and macro make a .mov file for a specified molecule.
# makemovie -f qt -o tamox.mov -c qt_anim -r 15 `ls -tr ../f*.tif`
print "DO NOT FORGET icmt -24; set view 10 10 640 480"
macro molkino i_tZoom (20) i_tRotate (20) l_preview (yes) R_startView R_endView s_Files ("/icmdata/movies/tamox/f")
GRAPHICS.ballQuality = 15
nfr=30
for i=0,i_tZoom*nfr
set view View(R_startView ,R_endView, 0.5-0.5*Cos(180.*i/Real(i_tZoom*nfr)))
if(!l_preview) write image s_Files + i
endfor
B = 0.
for i=0,i_tRotate*nfr
A = 360./Real(nfr*i_tRotate) * i
A = 180. - 180.*Cos(A/2.)
rotate view Rot({0. 1. 0.} A-B)
B = A
if(!l_preview) write image s_Files + (i_tZoom*nfr+ i)
endfor
endmacro
#read object "tamoxifen"
read object "propecia.ob"
set window 10 10 640 480
GRAPHICS.ballRadius=0.4
display xstick
color a_//c* green
color a_//h* white
read rarray "v0"
read rarray "v1"
set view v0
In this case, the process of making a molecular movie animating the trajectory can be split into two steps. The first step is a preparation of a series of images stored as separate disk files. Watch the ICM movie by the display movie command and select a range of frames you are going to include to the movie. There are two ways how a series of the molecular graphics images can be saved as tif or rgb formatted files. !_ Image collection (type I) The following molecular representations are allowed in this case: wire, cpk, ball, stick, xstick and ribbon . The image option of the ICM display movie command is required. An example:
build "alpha"
read movie "alpha"
display ribbon
color ribbon a_/1:9 magenta
color ribbon a_/10:18 green
print "Adjust the view, press ENTER to continue"
pause # Pause to adjust a view of the molecule
# start of the collection of the image disk files
# (note, tif files are to be saved)
nframe = Nof(frame)
print "Total number of frames = ", nframe
# specify the range you need, for example:
ifrom = 10
ito = 20
# otherwise, for all frames:
# ifrom = 1
# ito = nframe
display movie ifrom ito image
Computationally more expensive
skin
and
surface
molecular representations (or a combination of any of these two with
those mentioned above) require an ICM script, as in the following example.
!_ Image collection (type II) build "alpha" read movie "alpha" display xstick a_//n,ca,c set window 600 30 640 480 # good to convert it later into NTSC format # change 640 480 to appropriate dimensions for PAL lineWidth = 3. print "Adjust the view, press ENTER to continue" pause nframe = Nof(frame) print "Total number of frames = ", nframe ifrom = 10 ito = 20 icount = 0 l_confirm = no IMAGE.compress = yes for iframe = ifrom, ito load frame iframe icount = icount + 1 imgname = s_tempDir + "alpha_" + String(icount-1) display xstick a_//n,ca,c green display surface a_/7:12/!n,ca,c a_/7:12/!n,ca,c magenta write image imgname undisplay surface # should be removed and redisplayed at the next step endfor Whatever protocol you make use of, a series of files should appear in the s_tempDir directory. List their names in a file, for example, alpha.lst: /usr/tmp/alpha_0.tif /usr/tmp/alpha_1.tif /usr/tmp/alpha_2.tif /usr/tmp/alpha_3.tif /usr/tmp/alpha_4.tif /usr/tmp/alpha_5.tif /usr/tmp/alpha_6.tif /usr/tmp/alpha_7.tif /usr/tmp/alpha_8.tif /usr/tmp/alpha_9.tif(Note, image numbers are started from zero, and "_" (underscore) is inserted before the current frame number.) Now, you can put these image files into a movie file. We suggest to use the makemovie command for Silicon Graphics machines. The following is a sample UNIX-shell command line which should be entered to make a non-interlaced MPEG-formatted movie with the frame size 640 by 480 saved in the Apple QuickTime movie file alpha.qt: makemovie -f qt -o alpha.qt -c qt_anim -s 640,480 -r 30 ` cat alpha.lst` Upon completion, use the movieplayer IRIX command to see the movie. UNIX man on-line help should allow you to learn more about these (and other) helpful commands. And let us give you several helpful hints:
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