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@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@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@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