PyMOL tutorial 4 : Making Movies

Expand the description for timings. - https://github.com/PyMOL-Ross This is an introduction to movies in PyMOL This is a rough edit from a tutorial. Links https://www.pymolwiki.org/index.php/M... https://pymolwiki.org/index.php/Mview from the start : a little intro, additional software 00:02:18 : movies with the GUI 00:08:51 : using states in the GUI 00:10:22 : using scenes in the GUI 00:13:36 : movies on the command line - mset & mview 00:19:45 : using states on the command line 00:26:06 : using 'morph' and 'create' in movies 00:31:52 : using scenes on the command line 00:37:12 : other examples from the net Additional software RECOMMENDED- Pymol makes BIG movie files. This software compresses files without losing resolution Handbrake using RF 24 ########## 00:02:18 # USING THE GUI TO MAKE A MOVIE rein fetch 2chb, async=0 remove hydrogen hide all bg_color white select lig, organic select bb, bb. select sc, sc. + name ca + /*//*/PRO`*/N as cartoon, bb show sticks, sc + lig util.cbc color black, lig util.cnc orient bb select none dist hbbb, org, bb, mode=2 dist hbsc, org, sc, mode=2 color grey20, hbbb color grey80, hbsc hide labels Appending multiple gui camera controls that look good! orient Movie ~ Program ~ Camera loop ~ Nutate ~ 30deg.4sec Movie ~ append ~ 2s orient c. D Movie ~ Program ~ Camera loop ~ Nutate ~ 30deg.4sec Movie ~ append ~ 2s orient c. D & org Movie ~ Program ~ Camera loop ~ Nutate ~ 30deg.4sec Movie ~ append ~ 2s mplay ########### 00:08:51 # cycle through my NMR/MD/morph/other states!! rein fetch 2adt, async=0 as sticks Movies ~ Program ~ state loop ~ Full speed Can just 'save as movie' I want my states to cycle while i move around the structure Well, you can’t do that in the GUI, sorry! (at least i dont know how) ############ 00:10:22 # GUI scenes # scenes are amazing! make scenes with Scene ~ Store ~ F? Movie ~ Program ~ Scene loop ~ Nutate ~ 30deg.4sec Can be a bit clunky to use but your creative skills can get around this. ########### 00:13:36 # Movies on the command line what is mset mset 1 x200 (x[num]) append frames at given state if you have states too mset 1 -200 (-[num]) move between states (while moving between frames) mset 1 200 ([num]) moves straight to numbered state So, you can make some fancy movies of MD simulations, NMR, morphs! ########### what is mview #examples Ligand zoom rein fetch 1rx1, async=0 as cartoon as sticks, organic mset 1 x150 orient mview store, 1 mview store, 50 orient organic mview store, 100 mview store, 150 commands don't have to be in sequencial order. 360° rotation rein fetch 1rx1, async=0 as cartoon as sticks, organic mset 1 x180 mview store, 1 mview store, 180 turn y, 120 mview store, 60, power=1.0 turn y, 120 mview store, 120, power=1.0 ############ 00:19:45 # Moving through states while moving the camera rein load xxx.pse # load a file with states for this one. dress structure representations appropriately for video mview reset orient mset 1 x50 -500 x50 mview interpolate mview smooth mview store, 1 turn x, -90 mview store, 50 mview store, 150 turn x, 90 mview store, 250 mview store, 350 turn y, 90 mview store, 450 mview store, 550 ############## 00:26:06 # Movies on the command line with state control and morph 'morph' - available on pymol-2.x - transitions between structures 'create' - separates and merges objects and states have a go with morph and create, my comments below rein remove hydrogen hide all bg_color white select lig, organic select bb, polymer & name c+o+n+ca select sc, sc. + name ca + /*//*/PRO`*/N as cartoon, bb show sticks, sc + lig util.cbc color black, lig util.cnc orient bb dss create pent1, reduced, 1, 1 create mono1, reduced & s. PROA, 1, 1 create mono2, reduced & s. PROB, 1, 1 create mono3, reduced & s. PROC, 1, 1 create mono4, reduced & s. PROD, 1, 1 create mono5, reduced & s. PROE, 1, 1 Move and denature extract pent2, mono* delete mono* morph morphname, pent2, pent1, refinement=1, steps=100 create fullmodel, morphname, 0, 1 smooth reduced, 10, 10 create fullmodel, reduced, 0, 101 ########### 00:31:52 # Movies on the command line with scenes With scenes you can change representations during the movie you'll need an input structure with +380 states ########### THIS CAN ACT AS A GOOD TEMPLATE!! mview reset mset 1 x400 -380 x20 set scene_animation,-1 set scene_animation_duration,0 mview interpolate mview smooth set representation and store scenes scene 001, store blar blar blar scene 002, store etc. . . . control the camera interacting with the frames scene 001 mview store, 1 turn x, -120 mview store, 50, power=1.0 turn x, -120 mview store, 100, power=1.0 turn x, -120 mview store, 150 scene 002 etc. . . . mview interpolate mview smooth rewind ############# Movies and molecular transitions in powerpoint (Sorry youtubers, this bit has some unpublished work in it) 00:37:12 # check the internet for further examples