[Chimera-users] Chimera movie question

Thomas Goddard goddard at cgl.ucsf.edu
Mon Jan 25 10:15:03 PST 2010

 > OK, thanks Tom.  Any tips on how to do all three planes at once - or
 > rather keep the others constant while eating though the side plane.  I
 > have sen movies like this but can;t seem to figure out how to do it in
 > Chimera.
 > Bridget

Hi Bridget,

   Oh, now I understand what you meant by 3 planes.  The only way to 
show orthogonal planes is to open additional copies of the volume and 
show the needed planes with those copies.  A trouble you will encounter 
with this is that Chimera does not handle more than one transparent 
models correctly.  So it may appear that a plane in back is actually 
drawn on top of a plane in front.  To avoid this you can make some of 
the planes opaque using the Solid Rendering Options panel of the volume 
dialog to switch to color mode to single-color opaque.  Another way to 
handle it is load the models in such a way that the lowest model number 
is the back-most plane -- that will assure it is drawn first, and higher 
model id numbers will get drawn in front of that.  I use the opaque 
setting instead.


-------- Original Message --------
Subject: Re: [Chimera-users] Chimera movie question
From: Tom Goddard <goddard at cgl.ucsf.edu>
To: Bridget Carragher <bcarr at scripps.edu>
Date: 1/24/10 9:54 PM

> Hi Bridget,
>  Unfortunately the wait command without specifying a number of frames 
> does not work correctly for the volume planes command.  I'll record a 
> request to fix this.  So you have to specify the number of frames to 
> wait.  It should work if you specify 201 frames to wait since you are 
> showing planes 200 to 0.  To show 3 adjacent planes the last paramter 
> should be 3.  So the commands are:
>    volume #1 planes z,200,0,1,3
>    wait 201
> I tried this and it worked correct in the current Chimera daily build.
>    Tom
>> Hi Chimera Team,
>> I am sure this is a super dumb question but I have searched the 
>> documentation quite extensively and can;t seem to find a solution.  I 
>> am trying to make a movie where I move through a tomogram in planes 
>> using the command:
>> volume #1 planes z,200,0,1,1
>> wait
>> But the wait does not seem to work - it just skips right to the next 
>> command and gets all snarled up.  I can explicitly put in the number 
>> of frames but then the timing of the movie is all messed up.
>> Any suggestions much appreciated.
>> I also would rather be showing all 3  planes at the same time while I 
>> movie through the slab this but I can;t seem to find the right command 
>> to do that in a script.
>> Thanks for any help you can provide,
>> Best regards,
>> Bridget
>> ---------------------------------------------------------------------------------------------------------------------------------- 
>> Bridget Carragher, Associate Professor
>> Automated Molecular Imaging Group, Department of Cell Biology
>> The Scripps Research Institute, MC CB129,10550 North Torrey Pines 
>> Road, La Jolla, CA 92037
>> National Resource for Automated Molecular Microscopy: 
>> http://nramm.scripps.edu
>> ---------------------------------------------------------------------------------------------------------------------------------- 
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