<div dir="ltr"><div dir="ltr">Dear Elaine and Tom, <div><br></div><div>Thanks a lot for the fantastic effort and time. </div><div><br></div><div>Since the updating the centre was the issue, I took the zone @ca route, script is the following </div><div><br></div><div><div>------------------------------------------------------------------------</div><div># Open maps and set threshold</div><div>open start_resample_lp30_scaled.mrc </div><div>open end_lp30.mrc </div><div>open RZQS_open2.pdb</div><div>open RZQS2.pdb </div><div><br></div><div>vol all step 1</div><div><br></div><div>vol #0 level 0.026</div><div>vol #1 level 0.026</div><div><br></div><div># Create morph volume #4</div><div>vop morph #0,1 frames 0 model #4 </div><div>#vol #4 level 0.02</div><div><br></div><div># Create morph models model #5</div><div>morph start #2 frames 100</div><div>morph interpolate #3 </div><div>morph movie </div><div><br></div><div>## color the chains, so that scolor takes it to the map</div><div>color #999999999999 #</div><div>color #00002f68f684 #:.L</div><div>color #25edbda038e3 #:.N #:.B</div><div>color #ffff00000000 #:.Z #:.S #:.Q</div><div>color #999900009999 #:.R</div><div><br></div><div><br></div><div><br></div><div># Color near marker</div><div>perframe "scolor #4 zone @ca range 15"<br></div><div><br></div><div><br></div><div>#Play morph</div><div><br></div><div>coordset #5 1,100; vop morph #0,1 start 0 playstep 0.01 frames 100 interpolateColors false model #4</div></div><div>----------------------------------------------------------------------</div><div><br></div><div>Above script actually works, but </div><div><br></div><div>1) there is a small delay between PDB and map</div><div>2) Morph looks too slow</div><div>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. </div><div><br></div><div>Any help regarding above three would make my weekend :). </div><div><br></div><div>One again thank you so much for your time and effort.</div><div><br></div><div>best regards</div><div>Rajan </div><div><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Sep 14, 2018 at 8:11 PM, Elaine Meng <span dir="ltr"><<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Rajan,<br>
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:<br>
<br>
# map models #0,1<br>
open emdbID:1283<br>
open emdbID:1284<br>
<br>
# atomic models #2,3<br>
open 2gbp<br>
open 2fwo<br>
mm #3 #2<br>
<br>
# atomic morph trajectory #4<br>
morph start #2 frames 99<br>
morph interpolate #3<br>
morph movie<br>
<br>
# play atomic trajectory<br>
~modeldisp #2,3<br>
coordset #4 1,100<br>
<br>
# create and show map morph #5<br>
vop morph #0,1 frames 100 playstep .01 mod #5<br>
<br>
# try measuring current frame of trajectory and doing color zone<br>
measure center #4 mark true rad 2 color red mod #6; scolor #5 zone #6 range 25<br>
<br>
# now do everything at once while morphing<br>
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<br>
<br>
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.<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<div class="HOEnZb"><div class="h5"><br>
> On Sep 13, 2018, at 6:09 PM, Tom Goddard <<a href="mailto:goddard@sonic.net">goddard@sonic.net</a>> wrote:<br>
> <br>
> Hi Rajan,<br>
> 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.<br>
> <br>
> <a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html" rel="noreferrer" target="_blank">https://www.cgl.ucsf.edu/<wbr>chimera/docs/UsersGuide/midas/<wbr>perframe.html</a><br>
> <br>
> 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.<br>
> Tom<br>
> <br>
>> On Sep 13, 2018, at 6:54 AM, Rajan Prabu <<a href="mailto:jrajanprabu@gmail.com">jrajanprabu@gmail.com</a>> wrote:<br>
>> <br>
>> Hello again, <br>
>> <br>
>> Following another old thread, <br>
>> <br>
>> <a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-September/012743.html" rel="noreferrer" target="_blank">http://plato.cgl.ucsf.edu/<wbr>pipermail/chimera-users/2016-<wbr>September/012743.html</a><br>
>> <br>
>> I could morph/play the coordinates and Volume at the same time. The script is given below. <br>
>> <br>
>> ------------------------------<wbr>----------------------<br>
>> # Open maps and set threshold<br>
>> open 1.mrc<br>
>> open 2.mrc<br>
>> open start_full.pdb<br>
>> open end_full.pdb<br>
>> <br>
>> vol #0,1 level .025<br>
>> <br>
>> # Create a marker for coloring<br>
>> measure center #2 mark true radius 20 color red<br>
>> ~display #4<br>
>> <br>
>> # Create morph volume<br>
>> vop morph #0,1 frames 0 model #5<br>
>> <br>
>> # Create morph models model #6<br>
>> morph start #2 frames 200<br>
>> morph interpolate #3 frames 200<br>
>> morph movie<br>
>> <br>
>> # marker on morph<br>
>> measure center #6 mark true radius 20 color red<br>
>> <br>
>> # Color near marker<br>
>> scolor #5 zone #6 range 50<br>
>> <br>
>> coordset #6 1,100; vop morph #0,1 start 0 playstep 0.01 frames 100 model #6<br>
>> ------------------------------<wbr>----------------------<br>
>> <br>
>> <br>
>> 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. <br>
>> <br>
>> Thanks in advance for your time and help.<br>
>> <br>
>> best regards<br>
>> Rajan <br>
<br>
</div></div></blockquote></div><br></div>