[Chimera-users] Morph colors

[Elaine Meng]

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