[Chimera-users] Morph colors

Fri Sep 14 12:47:07 PDT 2018

Well, “delay” and “too slow” may be in the rendering capabilities the computer.  If you saved a movie the time issues might not show up in the actual playing of the movie. However, if you wanted fewer steps/frames in the whole process, you would use a larger playstep and fewer frames in the atomic and map morphs.

To make a movie file, you would put “movie record” command (with various options) in the script where you want to start recording and “movie encode” (also with options) at the end.  The latter has options for “roundtrip” (to include playing the whole thing backwards) and playback “framerate".  Probably it will take some trial and error to get what you want.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html>

We have several examples of movie-making scripts,  It can get pretty fancy, with titles etc.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples>

I hope this helps,
Elaine

> On Sep 14, 2018, at 12:29 PM, Rajan Prabu <jrajanprabu at gmail.com> wrote:
> 
> Dear Elaine and Tom, 
> 
> Thanks a lot for the fantastic effort and time. 
> 
> Since the updating the centre was the issue, I took the zone @ca route,  script is the following 
> 
> ------------------------------------------------------------------------
> # Open maps and set threshold
> open start_resample_lp30_scaled.mrc  
> open end_lp30.mrc  
> open  RZQS_open2.pdb
> open  RZQS2.pdb 
> 
> vol all step 1
> 
> vol #0 level 0.026
> vol #1 level 0.026
> 
> # Create morph volume #4
> vop morph #0,1 frames 0 model #4 
> #vol #4 level 0.02
> 
> # Create morph models  model #5
> morph  start #2 frames 100
> morph interpolate #3  
> morph movie  
> 
> ## color the chains, so that scolor takes it to the map
> color #999999999999 #
> color #00002f68f684  #:.L
> color #25edbda038e3 #:.N #:.B
> color #ffff00000000 #:.Z #:.S #:.Q
> color #999900009999 #:.R
> 
> 
> 
> # Color near marker
> perframe "scolor #4 zone @ca range 15"
> 
> 
> #Play morph
> 
> coordset #5 1,100; vop morph #0,1 start 0 playstep 0.01 frames 100  interpolateColors false model #4
> ----------------------------------------------------------------------
> 
> Above script actually works, but 
> 
> 1) there is a small delay between PDB and map
> 2) Morph looks too slow
> 3 ) I would like to show open and close confirmation at least twice. meaning forward as the script above and reverse ( 2x)  and  record that as a movie. 
> 
> Any help regarding above three would make my weekend :). 
> 
> One again thank you so much for your time and effort.
> 
> best regards
> Rajan 
> 
> 
> On Fri, Sep 14, 2018 at 8:11 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Rajan,
> With some help from Tom, I think I finally figured out the commands to mark morphing atoms at each step and color a simultaneously morphing map by zone around the marker for that time step.  The following commands are a fake example (the atoms don’t really go with the maps) but they show how it can be done:
> 
> # map models #0,1
> open emdbID:1283
> open emdbID:1284
> 
> # atomic models #2,3
> open 2gbp
> open 2fwo
> mm #3 #2
> 
> # atomic morph trajectory #4
> morph start #2 frames 99
> morph interpolate #3
> morph movie
> 
> # play atomic trajectory
> ~modeldisp #2,3
> coordset #4 1,100
> 
> # create and show map morph #5
> vop morph #0,1 frames 100 playstep .01 mod #5
> 
> # try measuring current frame of trajectory and doing color zone
> measure center #4 mark true rad 2 color red mod #6; scolor #5 zone #6 range 25
> 
> # now do everything at once while morphing
> vop morph #0,1 frames 100 playstep .01 mod #5; perframe "measure center #4 mark true rad 2 color red mod #6; scolor #5 zone #6 range 25; delete #6"; coordset #4 1,100;wait 100; ~perframe
> 
> The main trick for me was putting the “vop morph” before the “perframe”.  If I did it the other way around, the zone coloring wasn’t shown.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Sep 13, 2018, at 6:09 PM, Tom Goddard <goddard at sonic.net> wrote:
> > 
> > Hi Rajan,
> >   Yes, you would have to measure the center for each frame and use that for the zone coloring.  In order to perform a command or sequence of commands each frame you use the “perframe” command.
> > 
> >       https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html
> > 
> > Elaine Meng said she tried it and did not get your case to work though, so there may be some unexpected difficulties.  But you should try it.
> >       Tom
> > 
> >> On Sep 13, 2018, at 6:54 AM, Rajan Prabu <jrajanprabu at gmail.com> wrote:
> >> 
> >> Hello again, 
> >> 
> >> Following another old thread, 
> >> 
> >> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-September/012743.html
> >> 
> >> I could morph/play the coordinates and Volume at the same time. The script is given below. 
> >> 
> >> ----------------------------------------------------
> >> # Open maps and set threshold
> >> open 1.mrc
> >> open 2.mrc
> >> open  start_full.pdb
> >> open end_full.pdb
> >> 
> >> vol #0,1 level .025
> >> 
> >> # Create a marker for coloring
> >> measure center #2 mark true radius 20 color red
> >> ~display #4
> >> 
> >> # Create morph volume
> >> vop morph #0,1 frames 0 model #5
> >> 
> >> # Create morph models  model #6
> >> morph  start #2 frames 200
> >> morph interpolate #3  frames 200
> >> morph movie
> >> 
> >> # marker on morph
> >> measure center #6 mark true radius 20 color red
> >> 
> >> # Color near marker
> >> scolor #5 zone #6 range 50
> >> 
> >> coordset #6 1,100; vop morph #0,1 start 0 playstep 0.01 frames 100 model #6
> >> ----------------------------------------------------
> >> 
> >> 
> >> Still the color is at centre of of the first Frame of morph.  If I understand correct I have to measure the centre for each Frame and  add marker and color it. But I still can't make it. Any help/directions in this regard would be very helpful.  
> >> 
> >> Thanks in advance for your time and help.
> >> 
> >> best regards
> >> Rajan 
> 
> 
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