[Chimera-users] Morph colors

[Rajan Prabu]

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
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180914/c556b158/attachment.html>