Movies & Scripts with MacPyMol - Institute for Molecular Virology
Movies & Scripts with MacPyMol - Institute for Molecular Virology
Movies & Scripts with MacPyMol - Institute for Molecular Virology
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<strong>Movies</strong> & <strong>Scripts</strong> <strong>with</strong><br />
<strong>MacPyMol</strong><br />
HELP! - PyMol Wiki<br />
http://www.pymolwiki.org<br />
B I O C H E M 6 6 0 - 2 0 1 1<br />
http://www.pymolwiki.org<br />
HELP! – PyMol Wiki<br />
<strong>Movies</strong> <strong>with</strong>in PyMol<br />
mset 1!<br />
mset defines which “state” (MODEL) is used<br />
!<br />
mdo 1: turn y,5;!<br />
turn = the action<br />
Y = the axis<br />
5 = number of degrees per turn<br />
mdo = action list on which “state”<br />
…/index.php/MovieSchool<br />
http://www.pymolwiki.org/<br />
index.php/Making_<strong>Movies</strong><br />
PyMol movies Suitable <strong>for</strong> Export<br />
Saving movie as MPG<br />
mclear!<br />
!<br />
mset 1 x36!<br />
!<br />
movie.roll 1, 36!<br />
!<br />
mplay!<br />
!<br />
mstop!<br />
mclear = clears previous settings<br />
mset defines which “state” (MODEL) is used<br />
AND how many frames are in the movie: 36<br />
movie.roll = action<br />
1 = first frame<br />
36 = laste frame<br />
ASSUMED = y axis and 360* rotation
Saving the Movie as Frames<br />
!! Movie can be saved as individual frames to be<br />
assembled in 3 rd party software:<br />
!! QuickTimePro (Mac / PC / 29.99$)<br />
"! http://www.apple.com/quicktime/extending/<br />
!! VideoMach (PC – 3 price versions)<br />
"! http://www.gromada.com/<br />
!! ImageMagick (Open Source, free)<br />
"! http://www.imagemagick.org/<br />
!! Avidemux (Open Source, free)
movie.screw<br />
movie.nutate<br />
!<br />
mclear!<br />
mset 1 x120!<br />
!<br />
movie.screw 1, 120!<br />
!<br />
mplay!<br />
mstop # to halt the movie<br />
!<br />
mclear!<br />
mset 1 x120!<br />
!<br />
movie.nutate 1, 120!<br />
!<br />
mplay!<br />
mstop # to halt the movie`<br />
Same as “lemniscate” in VMD<br />
Multiple PDB files: MODEL ENDMDL!<br />
Multiple PDB files: mset<br />
MODEL 1 !<br />
ATOM 1 O5' G A 1 -11.545 -12.549 4.261 1.00 0.00 O !<br />
ATOM 2 C5' G A 1 -12.281 -11.830 5.254 1.00 0.00 C !<br />
//!<br />
ATOM 768 H6 C A 24 -0.402 -19.203 3.575 1.00 0.00 H !<br />
TER 769 C A 24 !<br />
ENDMDL !<br />
MODEL 2 !<br />
ATOM 1 O5' G A 1 -10.937 -10.771 1.038 1.00 0.00 O !<br />
ATOM 2 C5' G A 1 -12.150 -10.309 1.638 1.00 0.00 C<br />
/ /<br />
ENDMDL !<br />
MODEL 3 !<br />
ATOM 1 O5' G A 1 -10.937 -10.771 1.038 1.00 0.00 O !<br />
ATOM 2 C5' G A 1 -12.150 -10.309 1.638 1.00 0.00 C<br />
/ /<br />
!<br />
!<br />
mset 1 -12 -1!<br />
MORPHS: 2RGX into 2RH5<br />
<strong>Scripts</strong><br />
File: all.pdb2 provided on scratch server<br />
2RGX: Adenylate Kinase from Aquifex Aeolicus in complex <strong>with</strong> Ap5A<br />
2RH5: Structure of Apo Adenylate Kinase from Aquifex Aeolicus<br />
!! Set of commands in a text file<br />
!! Activate on line command <strong>with</strong> @<br />
!! IF file ends <strong>with</strong> .pml :<br />
!! use menu File > Run
! Advanced:<br />
PyMol : Beyond Basic <strong>Movies</strong><br />
!! rTools<br />
http://www.rubor.de/pymol_extensions_de.html<br />
Last modified: Wed Apr 28, 2004<br />
!! eMovie PyMol plug-in<br />
http://www.weizmann.ac.il/ISPC/eMovie.html<br />
Last Updated: 02/04/2008<br />
Hodis, E., Schreiber, G., Rother, K., Sussman, J.L.,<br />
eMovie: a storyboard-based tool <strong>for</strong> making molecular movies,<br />
Trends in Biochemical Sciences 32, 199-204 (2007).<br />
<strong>Movies</strong> <strong>with</strong> PyMol: 3 ways built in<br />
!!Scene Menu:<br />
!!Saved scenes in Function keys F1-F12<br />
!!Animate <strong>with</strong>in PyMol<br />
!!Animate Script command<br />
!!can export frames/QuickTime<br />
!!Other ways <strong>with</strong> external scripts or<br />
plug-ins.<br />
<strong>Movies</strong> – Scene menu<br />
Scene Export<br />
Scene Export<br />
Scene Export - Saving movie as MPEG
Scene Export<br />
Scene Export<br />
– Example F1-F4 –<br />
PyMol External GUI Text Echo Window<br />
Movie: frame 1 of 938, 0.18 sec. (0:02:50 - 0:02:50 to go).<br />
Movie: frame 2 of 938, 0.18 sec. (0:02:47 - 0:02:48 to go).<br />
Movie: frame 3 of 938, 0.19 sec. (0:02:58 - 0:02:51 to go).<br />
. . . . . .<br />
Movie: frame 937 of 938, 0.19 sec. (0:00:00 - 0:00:00 to go).<br />
Movie: frame 938 of 938, 0.18 sec. (0:00:00 - 0:00:00 to go).<br />
produce: creating '/Users/dmc/Desktop/PyMol_F12345.mpg' (in background)...<br />
produce: 126976 bytes written...<br />
produce: 5828608 bytes written...<br />
produce: 15331328 bytes written...<br />
produce: 15527936 bytes written...<br />
produce: finished.<br />
F1-2-3-4 / 4sec / Steady / 9.8 Mb / MPEG<br />
Scene Export<br />
– Example F1-F5 –<br />
Ambient Occlusion (PyMol 1.4)<br />
F1-2-3-4-5 / 4sec / Y-Rock / 14.8 Mb / MPEG<br />
Ambient occlusion attempts to approximate the way light radiates in real life,<br />
especially off what are normally considered non-reflective surfaces.<br />
https://secure.wikimedia.org/wikipedia/en/wiki/Ambient_occlusion<br />
Optional Tutorials: VMD<br />
1)! ."<br />
Creating <strong>Movies</strong> (Automatically) <strong>with</strong> VMD<br />
The tutorials can be downloaded<br />
from:<br />
http://virology.wisc.edu/acp<br />
Click on “Class Tutorials”<br />
Then under “Our Tutorials” use<br />
the pull-down menu to select the<br />
PDF you want to download. It will<br />
open automatically in your<br />
browser.<br />
To save simply use the<br />
“Save As” command from the File<br />
menu in the browser.<br />
2)! ."
VMD: Required software <strong>for</strong> movie making:<br />
Mac / Unix / Linux<br />
!! Imagemagick (free)<br />
!! NetPbm (free)<br />
!! Install <strong>with</strong> either:<br />
!! Fink (free)<br />
!! MacPort (free)<br />
Note: QuickTimePro<br />
( Mac /Win ) is $29<br />
VMD: Required software <strong>for</strong> movie making:<br />
Windows<br />
Note: QuickTimePro<br />
For Windows is $29<br />
!! VideoMach is required <strong>for</strong> Windows VMD<br />
!! 3 versions:<br />
"! FREE: ($0) But overlays a textual banner over the output<br />
video. Banner disappears after one second.<br />
"! Standard ($25 <strong>for</strong> non-commercial) - Banner can still appear<br />
if you're opening or saving file types reserved <strong>for</strong> the<br />
Professional Mode.<br />
"! Professional ($75) – no restrictions<br />
!! http://gromada.com/videomach/<br />
!! Note: You can also make individual frames and<br />
combine them <strong>with</strong> QuickTime Pro (29.99$)<br />
VMD “automatic” movies<br />
Today<br />
! Pymol 2<br />
page 99<br />
-!VMD –optional online tutorials<br />
1NYZ<br />
Acridine in DNA
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