Sorry, I made a mistake and found my problem. All the best JD Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es ----- Missatge original ----- De: chimera-users-request@cgl.ucsf.edu Data: Divendres, Octubre 24, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 66, Issue 22
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Today's Topics:
1. volume planes display loop (Benoit Zuber) 2. Re: volume planes display loop (Tom Goddard)
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Message: 1 Date: Fri, 24 Oct 2008 16:36:42 +0100 From: Benoit Zuber <bzuber@mrc-lmb.cam.ac.uk> Subject: [Chimera-users] volume planes display loop To: chimera users list <chimera-users@cgl.ucsf.edu> Message-ID: <4901EB8A.9040102@mrc-lmb.cam.ac.uk> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi,
I have got some questions regarding plane display of volumes: Is there a way to cycle through a limited range of planes? For example if the thickness of my volume is 300, is it possible to cycle from z = 100 to z = 120, instead of from z = 0 to z = 299?
Is there a way to make the cycling through the planes start in the other direction than when it stopped last time? For example, I click stop while the display is cycling from low z value to high z value. If I then click start, the display is going to cycle again from low to high z value but I would like it to cycle from high to low z value.
Is it possible to specify a starting plane and an end plane, and to have the display going from the starting plane to the end plane only once (without cycling)?
Finally, can all of this be specified through the command line?
Cheers, Ben
Beno?t Zuber MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH United Kingdom +44 1223 402209 bzuber@mrc-lmb.cam.ac.uk
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Message: 2 Date: Fri, 24 Oct 2008 10:31:44 -0700 From: Tom Goddard <goddard@cgl.ucsf.edu> Subject: Re: [Chimera-users] volume planes display loop To: Benoit Zuber <bzuber@mrc-lmb.cam.ac.uk> Cc: chimera users list <chimera-users@cgl.ucsf.edu> Message-ID: <49020680.2070802@cgl.ucsf.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Ben,
The current Chimera daily builds have a more flexible volume plane cycling interface. In the planes panel it now has a switch
Cycle through [20] planes at speed [30]
It lets you play through a specified number of planes centered on the currently shown plane. You start it by clicking a switch and stop it the same way. There is no control to stop after N planes, and the initial direction of play is the same as when you last stopped playback. There is currently no Chimera command equivalent which would obviously be handy for making movies. I've attached a Python script which can be used with Chimera commands (example given in script) to control exactly which frames to show in a movie. Note that the frame rate is only relevant for real-time cycling in Chimera. Movie recording captures every new frame no matter how slow they are rendered and plays in a movie player at 25 frames per second (adjustable with a movie encode command option). Chimera movie recording capabilities are very limited now but it is an area we intend to improve.
Tom
Benoit Zuber wrote:
Hi,
I have got some questions regarding plane display of volumes: Is there a way to cycle through a limited range of planes? For example if the thickness of my volume is 300, is it possible to cycle from z = 100 to z = 120, instead of from z = 0 to z = 299?
Is there a way to make the cycling through the planes start in the other direction than when it stopped last time? For example, I click stop while the display is cycling from low z value to high z value. If I then click start, the display is going to cycle again from low to high z value but I would like it to cycle from high to low z value.
Is it possible to specify a starting plane and an end plane, and to have the display going from the starting plane to the end plane only once (without cycling)?
Finally, can all of this be specified through the command line?
Cheers, Ben
Beno?t Zuber MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH United Kingdom +44 1223 402209 bzuber@mrc-lmb.cam.ac.uk
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End of Chimera-users Digest, Vol 66, Issue 22 *********************************************