Hi Kyle, This problem is mysterious. Never saw anything like it. Do the missing models #18 and #14 appear in the movie if you don't use raytracing? It could be a raytracing error. If you run just part of your script without movie recording up to the point where model 18 is displayed, then try File / Save Image and enable raytracing, does that raytraced image show model 18? Are models 18 and 14 atomic models? What display style? stick? sphere? ribbon? wire? Are any of the models 0 - 18 transparent? Chimera has trouble with more than one transparent model, although I would not expect that to be a problem raytracing a movie. By the way the "modeldisplay#N" commands should have a space before the "#". The command is "modeldisplay" and "#N" is the argument. I am amazed that works without a space, but I tested and it does work and I don't think that is related to your missing models. Tom -------- Original Message -------- Subject: [Chimera-users] Image not appearing From: MIKALS,KYLE A <kmikals@ufl.edu> To: chimera-users@cgl.ucsf.edu Date: 8/27/09 7:58 AM

I made a code to make movie and two of the molecules are not appearing in the saved output images. I put in the code where to save them so if something went wrong.

This is the code I made and models 18 and 14 display in the window while the code is running, but not in the saved images. I have no idea what is going wrong. Any ideas? Here is my code below.

# start capturing frames, in .png format movie record fformat png raytrace true directory /msg/users/kmikals/Chimera_Files #Created Label saying AAV Capsid Assembly

2dlabels create lab1 text 'AAV Capsid Assembly' color khaki size 28 xpos .2 ypos .94 visibility show

scale 1.008 50

#Starts action once previous command is complete

wait

modeldisplay#0 wait 5

turn y -1 35

wait 30

modeldisplay#17 turn y -.6 20

wait 30

modeldisplay#18 wait 30

turn y +1.4 35

wait 30

modeldisplay#3 ~modeldisplay#0 ~modeldisplay#17 ~modeldisplay#18

wait 30

scale 0.992 50

wait 15

turn y -1 65

wait 9

modeldisplay#4

wait 9

turn y -1 35

modeldisplay#5

wait 9

turn y -1 65

modeldisplay#10

wait 9

modeldisplay#9

wait 9

turn y -1 65

modeldisplay#14

wait 9

modeldisplay#11

wait 9

turn y -0.5 30

modeldisplay#12

wait 9

turn y -1 65

modeldisplay#13

wait 9

modeldisplay#6 turn y -1 65

wait 9

modeldisplay#7

wait 9

modeldisplay#8

2dlabels delete lab1

#hide_all_molecules

~modeldisplay#3

~modeldisplay#4

~modeldisplay#5

~modeldisplay#6

~modeldisplay#7

~modeldisplay#8

~modeldisplay#9

~modeldisplay#10

~modeldisplay#11

~modeldisplay#12

~modeldisplay#13

~modeldisplay#14 wait 20

scale 0.987

modeldisplay#16 turn y -.3 20 wait turn x -.75 35 wait 30 turn x .75 35 wait 30 turn x -.38 35 wait turn y -1 35 wait 30 turn y 2 180 wait turn x 2 180 wait # stop recording frames movie stop # write status information to reply log movie status # encode a movie in mp4 format from recorded frames movie encode mformat mp4 output /msg/users/kmikals/Chimera_Files

-- MIKALS,KYLE A Biochemistry University of Florida

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