volume planes tool
hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff
Hi Jeff, That's definitely a Tom Goddard question, but he is away on vacation this week. Pending a definitive answer, I am guessing it is not in the plans. However, I believe you can do what you want by resampling the data on a differently oriented grid, and then using the "Planes" feature on that second, resampled set of data. You would generate the resampled data using the "Subregion selection" feature of Volume Viewer, by turning on "Select subregions..." with the mouse, and after drawing the selection box, turning on "Rotate selection box" and change the orientation as desired, then clicking the Resample button. This does not mess up your original data, just creates an additional, resampled data set. Downsides are that it may take some coordination or a couple of tries to rotate the box as desired, and resampling causes some loss of resolution. It may be that resampling is necessary for showing arbitrarily oriented planes, however, even if such an option were added to the GUI. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 7, 2008, at 10:07 AM, Jeff Triffo wrote:
anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff
yes, that would work but seems tedious for frequent use, and assumes the desired orientation is known. There is a capability in IMOD to do this "live" through their 3dmod Slicer viewer - which I have been assuming just does on-the-fly interpolation of the data, because it is a live update. It's an incredibly useful function to have access to because the user is often "hunting" for the right orientation for a slice, and I often find myself wanting it in Chimera. So I find myself doing quite a bit of pre-work modeling in 3dmod prior to being able to jump to Chimera. but, for now, I could just find desired orientations in IMOD, and try to reproduce that using a resampling of the entire volume in Chimera. In my case, that would require knowing the relationships between the Euler convention in 3dmod and Chimera, along with where each program defines the center of rotation (which I have looked into many times for various reasons - such as using IMOD models superimposed with volume displays in Chimera - but always forget soon after). -Jeff Elaine Meng wrote:
Hi Jeff, That's definitely a Tom Goddard question, but he is away on vacation this week.
Pending a definitive answer, I am guessing it is not in the plans. However, I believe you can do what you want by resampling the data on a differently oriented grid, and then using the "Planes" feature on that second, resampled set of data. You would generate the resampled data using the "Subregion selection" feature of Volume Viewer, by turning on "Select subregions..." with the mouse, and after drawing the selection box, turning on "Rotate selection box" and change the orientation as desired, then clicking the Resample button. This does not mess up your original data, just creates an additional, resampled data set.
Downsides are that it may take some coordination or a couple of tries to rotate the box as desired, and resampling causes some loss of resolution. It may be that resampling is necessary for showing arbitrarily oriented planes, however, even if such an option were added to the GUI.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Aug 7, 2008, at 10:07 AM, Jeff Triffo wrote:
anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff
Hi Jeff, Tom may add this to his requests list when he returns, but I can't make promises on his behalf! As you can see, the list is pretty long: http://www.cgl.ucsf.edu/chimera/plans.html Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 7, 2008, at 10:59 AM, Jeff Triffo wrote:
yes,
that would work but seems tedious for frequent use, and assumes the desired orientation is known. There is a capability in IMOD to do this "live" through their 3dmod Slicer viewer - which I have been assuming just does on-the-fly interpolation of the data, because it is a live update. It's an incredibly useful function to have access to because the user is often "hunting" for the right orientation for a slice, and I often find myself wanting it in Chimera. So I find myself doing quite a bit of pre-work modeling in 3dmod prior to being able to jump to Chimera.
but, for now, I could just find desired orientations in IMOD, and try to reproduce that using a resampling of the entire volume in Chimera. In my case, that would require knowing the relationships between the Euler convention in 3dmod and Chimera, along with where each program defines the center of rotation (which I have looked into many times for various reasons - such as using IMOD models superimposed with volume displays in Chimera - but always forget soon after).
-Jeff
Looking at Tom's "plans" page (http://www.cgl.ucsf.edu/chimera/plans.html ), I see this feature listed there (#57). According to the blurb for #57, Karin Gross and Christoph Best have written an extension called TomoPlane for doing this: Christoph Best: TomoPlane --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Aug 7, 2008, at 10:59 AM, Jeff Triffo wrote:
yes,
that would work but seems tedious for frequent use, and assumes the desired orientation is known. There is a capability in IMOD to do this "live" through their 3dmod Slicer viewer - which I have been assuming just does on-the-fly interpolation of the data, because it is a live update. It's an incredibly useful function to have access to because the user is often "hunting" for the right orientation for a slice, and I often find myself wanting it in Chimera. So I find myself doing quite a bit of pre-work modeling in 3dmod prior to being able to jump to Chimera.
but, for now, I could just find desired orientations in IMOD, and try to reproduce that using a resampling of the entire volume in Chimera. In my case, that would require knowing the relationships between the Euler convention in 3dmod and Chimera, along with where each program defines the center of rotation (which I have looked into many times for various reasons - such as using IMOD models superimposed with volume displays in Chimera - but always forget soon after).
-Jeff
Elaine Meng wrote:
Hi Jeff, That's definitely a Tom Goddard question, but he is away on vacation this week.
Pending a definitive answer, I am guessing it is not in the plans. However, I believe you can do what you want by resampling the data on a differently oriented grid, and then using the "Planes" feature on that second, resampled set of data. You would generate the resampled data using the "Subregion selection" feature of Volume Viewer, by turning on "Select subregions..." with the mouse, and after drawing the selection box, turning on "Rotate selection box" and change the orientation as desired, then clicking the Resample button. This does not mess up your original data, just creates an additional, resampled data set.
Downsides are that it may take some coordination or a couple of tries to rotate the box as desired, and resampling causes some loss of resolution. It may be that resampling is necessary for showing arbitrarily oriented planes, however, even if such an option were added to the GUI.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Aug 7, 2008, at 10:07 AM, Jeff Triffo wrote:
anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Jeff, I don't think I will work on arbitrary orientation volume slice planes until I improve speed of flipping through axis aligned planes. Here are some comments to give you a better idea of the issues. It is currently possible to get arbitrary volume planes in two ways, using the Resample button in the subregion selection panel, or the TomoPlane Chimera extension from Karen Gross and Christophe Best. Both of these approaches are somewhat clunky. The resample button requires you to press a button to get an updated view and creates a new volume on every press. The TomoPlane tool is rather slow to update and has too complex a user interface and does not work with the latest Chimera (I'll fix that soon). The main problem is performance and user interface. Axis aligned plane display with the volume dialog planes panel is a factor of several times slower than I'd like. Improving rendering speed when changing the plane will probably be achieved by not destroying the plane model with each new orientation, using texture rendering (not done by TomoPlane), preloading full data, using 3-d opengl textures when the graphics card has sufficient memory. The user interface should be simple, but it seems it will need another mouse mode to move the plane, and maybe some ability to have more than one plane, maybe show exact plane parameters (axis or angles), maybe allow marker placement on tilted planes. Would make sense to put these parameters in the current volume plane panel, but those planes do not require a separate volume model. The titled plane will need to be a separate model from the original volume. The optimization and user interface problems are difficult. I think improving the current axis-aligned plane rendering speed is more important. Also think reducing volume memory use in "solid" mode is more important. Also think volume mask support is more important. Plus there are quite a few other less closely related projects that I think have higher priority. All this means that improved support for tilted cut planes isn't likely to get much attention for at least several months. Tom Jeff Triffo wrote:
hi folks,
anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon?
-Jeff
Dear Colleague I am a new user of Chimera and I have a modest request. I have a mcr file and I would like to go through the volume of the object step by step. I have written a .cmd file for rotating the object as shown in the movie herewith. This was fairly easy . Now when it comes to slice the object progressively by conserving part of the volume I cannot see how to handle it. Would you be kind enough to help me? Looking forward to reading you Best regards Alain Gibaud -- *************************************** Alain GIBAUD Professeur LUNAM, Institut des Molécules et Matériaux du Mans (IMMM) UMR CNRS 6283 Université du Maine Avenue Olivier Messiaen,72085 Le Mans Cedex 9 – France Tél : +33 (0)2 43 83 32 62 Fax : +33 (0)2 43 83 35 18
Dear Alain, There are a few different related commands, but it depends on exactly which type of slicing you mean, whether only front/back, or at different angles, or whether you want to see only one plane of the volume data at a time. However, there are examples for each of these possibilities here: <http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html> Scroll down the to bottom section, click the images to play the short movies, and then click the links below them to see the corresponding commands and other details. The Chimera Animation Gallery has several longer movies and the command scripts for many of those, but they may not show the same things you are trying to do: <http://www.rbvi.ucsf.edu/chimera/animations/animations.html> General info on making movies in Chimera: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 22, 2016, at 10:40 AM, Alain Gibaud <Alain.Gibaud@univ-lemans.fr> wrote:
Dear Colleague I am a new user of Chimera and I have a modest request. I have a mcr file and I would like to go through the volume of the object step by step. I have written a .cmd file for rotating the object as shown in the movie herewith. This was fairly easy . Now when it comes to slice the object progressively by conserving part of the volume I cannot see how to handle it. Would you be kind enough to help me? Looking forward to reading you Best regards Alain Gibaud
participants (5)
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Alain Gibaud -
Elaine Meng -
Eric Pettersen -
Jeff Triffo -
Tom Goddard