Re: [Chimera-users] imod model viewing
Hi David, The Chimera IMOD model file reader only handles the meshes in the file. My guess is that the file you made does not contain meshes. Maybe it only has contour lines for the spheres. Or maybe the file format can contain geometric primitives like spheres without contour lines or meshes being specified. I don't know enough about IMOD to be sure. Tom David G. Morgan wrote:
Tom,
I was trying to use the new IMOD file reader and must be doing something foolish. I downloaded the newest chimera snapshot release (1.2392) and the imod.zip file and made a new installation. I can load my IMOD volume into chimera without any trouble. I then "opened" the IMOD model file (it opened as an "IMOD segmentation" type). That works without trouble, but I don't ever see the model. Even trying to use "focus" to bring it into the field of view gives me a blank field.
It's possible that my model is the wrong type - I'm playing with chimera in preparation for needing to do something fancy, so I simply created a set of spheres of different colors and different radii in IMOD, saved that model and tried to read it into chimera. I thought I'd simply be able to read this into chimera and see a couple of spheres, but I don't. I'm sure I'm doing something silly, but figured I'd bother you while I play around with it.
David Gene Morgan University of California at Davis
This brings up a related question, has anyone written a script to parse out IMOD model files for this information (point locations, and their connectivity for contours, followed by surfaces)? My understanding is that the mesh representation is an output format that is derived from the actual model data (above) that chimera does not currently import. best -Jeff Tom Goddard wrote:
Hi David,
The Chimera IMOD model file reader only handles the meshes in the file. My guess is that the file you made does not contain meshes. Maybe it only has contour lines for the spheres. Or maybe the file format can contain geometric primitives like spheres without contour lines or meshes being specified. I don't know enough about IMOD to be sure.
Tom
David G. Morgan wrote:
Tom,
I was trying to use the new IMOD file reader and must be doing something foolish. I downloaded the newest chimera snapshot release (1.2392) and the imod.zip file and made a new installation. I can load my IMOD volume into chimera without any trouble. I then "opened" the IMOD model file (it opened as an "IMOD segmentation" type). That works without trouble, but I don't ever see the model. Even trying to use "focus" to bring it into the field of view gives me a blank field.
It's possible that my model is the wrong type - I'm playing with chimera in preparation for needing to do something fancy, so I simply created a set of spheres of different colors and different radii in IMOD, saved that model and tried to read it into chimera. I thought I'd simply be able to read this into chimera and see a couple of spheres, but I don't. I'm sure I'm doing something silly, but figured I'd bother you while I play around with it.
David Gene Morgan University of California at Davis
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-- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488
Hi Jeff, The Chimera IMOD model file reader reads through all the data in the IMOD file but ignores everything except the meshes. Here is the file format specification I used to write the code http://bio3d.colorado.edu/imod/doc/binspec.html The Chimera Python code is in the IMOD directory obtained from the Chimera experimental features web page http://www.cgl.ucsf.edu/chimera/experimental/experimental.html in files IMOD/imod.py IMOD/imod_spec.py That code could be improved to display the contour data although Chimera does not have a high efficiency rendering of 1-dimensional curves. Using path tracer markers and links (equivalent to atoms and bonds) would consume alot of memory (a few kbytes per point). Tom
Tom, Thanks. That makes perfect sense. David Gene Morgan University of California at Davis 530 754 6891 -----Original Message----- From: Tom Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Tue 5/8/2007 4:31 PM To: David G. Morgan Cc: 'Chimera BB' Subject: Re: imod model viewing Hi David, The Chimera IMOD model file reader only handles the meshes in the file. My guess is that the file you made does not contain meshes. Maybe it only has contour lines for the spheres. Or maybe the file format can contain geometric primitives like spheres without contour lines or meshes being specified. I don't know enough about IMOD to be sure. Tom David G. Morgan wrote:
Tom,
I was trying to use the new IMOD file reader and must be doing something foolish. I downloaded the newest chimera snapshot release (1.2392) and the imod.zip file and made a new installation. I can load my IMOD volume into chimera without any trouble. I then "opened" the IMOD model file (it opened as an "IMOD segmentation" type). That works without trouble, but I don't ever see the model. Even trying to use "focus" to bring it into the field of view gives me a blank field.
It's possible that my model is the wrong type - I'm playing with chimera in preparation for needing to do something fancy, so I simply created a set of spheres of different colors and different radii in IMOD, saved that model and tried to read it into chimera. I thought I'd simply be able to read this into chimera and see a couple of spheres, but I don't. I'm sure I'm doing something silly, but figured I'd bother you while I play around with it.
David Gene Morgan University of California at Davis
Tom, I'm still trying to puzzle things out. There is an IMOD command that takes a model file and turns it into a mesh. When I run this on my model that was simple spheres, the starting and final files are identical and I still can't see anything in chimera. When I started with a more complex model (still a mix of spheres but also some contours), the conversion has an effect at the level of the binary data. However, I still don't see anything in chimera. I'm attaching that model to this e-mail. Can you take a look and make sure that your chimera also will not display it? I've renamed the file from "model.mod" to "model.doc" in the hope that if you have spam filters on your end, this will pass through the filters - around here, we can hardly trade work related files because of the filters! Also, if you can share the model you showed here Friday, would it be possible for you to e-mail it to me? Thanks for the help. David Gene Morgan University of California at Davis 530 754 6891 -----Original Message----- From: Tom Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Tue 5/8/2007 4:31 PM To: David G. Morgan Cc: 'Chimera BB' Subject: Re: imod model viewing Hi David, The Chimera IMOD model file reader only handles the meshes in the file. My guess is that the file you made does not contain meshes. Maybe it only has contour lines for the spheres. Or maybe the file format can contain geometric primitives like spheres without contour lines or meshes being specified. I don't know enough about IMOD to be sure. Tom David G. Morgan wrote:
Tom,
I was trying to use the new IMOD file reader and must be doing something foolish. I downloaded the newest chimera snapshot release (1.2392) and the imod.zip file and made a new installation. I can load my IMOD volume into chimera without any trouble. I then "opened" the IMOD model file (it opened as an "IMOD segmentation" type). That works without trouble, but I don't ever see the model. Even trying to use "focus" to bring it into the field of view gives me a blank field.
It's possible that my model is the wrong type - I'm playing with chimera in preparation for needing to do something fancy, so I simply created a set of spheres of different colors and different radii in IMOD, saved that model and tried to read it into chimera. I thought I'd simply be able to read this into chimera and see a couple of spheres, but I don't. I'm sure I'm doing something silly, but figured I'd bother you while I play around with it.
David Gene Morgan University of California at Davis
Hi David, Giovanni explained the problem well and gave good advice. For fun I enhanced the Chimera IMOD file reader to read the contours and points (which are just contours where the points are not connected). The new code is on the Chimera experimental features web page. http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Note that the contour reading is disabled by default because it is very slow, 10 - 100 times slower than reading the mesh. And it takes alot of memory. To enable it see the updated IMOD file reader documentation: http://www.cgl.ucsf.edu/chimera/experimental/imod/imod.html For the immune synapse segmentation I showed took about 5 minutes to load the contours and consumed about 1.5 Gbytes of memory. This is because each contour point is represented as a Chimera marker which is implemented as a molecule atom and consumes a few kbytes of memory. That data set has ~600,000 contour points. Your small test data set is plenty fast though. You can get the immune synapse segmentation I showed from the Cell Centered Data Base: http://ccdb.ucsd.edu/sand/main?event=displaySum&mpid=3632 The file you would want is (11 Mbytes): http://ccdb.ucsd.edu/sand/main?event=filedownload&filename=/telescience/home... Several people have expressed interest in plane by plane tomography segmentation in Chimera. In a month or a few Karin Gross's TomoViewer Chimera tool should be available which shows slices at arbitrary angles and perhaps will allow marker placement on the slices. Tom Giovanni Cardone wrote:
Hi, I am not really an expert of meshing in IMOD, but playing around with your file I get this impression: when I use imodmesh the program reports that the first 64 objects (spheres) are not meshed, and this is why you do not see anything in chimera; the remaining contours are meshed, but separately, because probably each contour is assigned to a separate object. This means that a mesh between these unconnected contours is not created, and hence chimera can not visualize it. If you use imodmesh with option -C (to cap off all unconnected contours), you can see the capping in chimera, but probably this is not what you want. My only advice is to try to generate multiple contours assigned to the same object, and see if it works. I hope this helps.
Giovanni
=============================================
Giovanni Cardone
Laboratory of Structural Biology Research
National Institutes of Health
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On May 10, 2007, at 3:43 PM, David G. Morgan wrote:
Tom,
I'm still trying to puzzle things out. There is an IMOD command that takes a model file and turns it into a mesh. When I run this on my model that was simple spheres, the starting and final files are identical and I still can't see anything in chimera. When I started with a more complex model (still a mix of spheres but also some contours), the conversion has an effect at the level of the binary data. However, I still don't see anything in chimera.
I'm attaching that model to this e-mail. Can you take a look and make sure that your chimera also will not display it? I've renamed the file from "model.mod" to "model.doc" in the hope that if you have spam filters on your end, this will pass through the filters - around here, we can hardly trade work related files because of the filters!
Also, if you can share the model you showed here Friday, would it be possible for you to e-mail it to me?
Thanks for the help.
David Gene Morgan University of California at Davis 530 754 6891
-----Original Message----- From: Tom Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Tue 5/8/2007 4:31 PM To: David G. Morgan Cc: 'Chimera BB' Subject: Re: imod model viewing
Hi David,
The Chimera IMOD model file reader only handles the meshes in the file. My guess is that the file you made does not contain meshes. Maybe it only has contour lines for the spheres. Or maybe the file format can contain geometric primitives like spheres without contour lines or meshes being specified. I don't know enough about IMOD to be sure.
Tom
David G. Morgan wrote:
Tom,
I was trying to use the new IMOD file reader and must be doing something foolish. I downloaded the newest chimera snapshot release (1.2392) and the imod.zip file and made a new installation. I can load my IMOD volume into chimera without any trouble. I then "opened" the IMOD model file (it opened as an "IMOD segmentation" type). That works without trouble, but I don't ever see the model. Even trying to use "focus" to bring it into the field of view gives me a blank field.
It's possible that my model is the wrong type - I'm playing with chimera in preparation for needing to do something fancy, so I simply created a set of spheres of different colors and different radii in IMOD, saved that model and tried to read it into chimera. I thought I'd simply be able to read this into chimera and see a couple of spheres, but I don't. I'm sure I'm doing something silly, but figured I'd bother you while I play around with it.
David Gene Morgan University of California at Davis
<model.doc> <mime-attachment.txt>
Hi David, This morning I changed the Chimera IMOD file reader again, putting contours and points for separate IMOD objects into separate Chimera marker sets. The way I had it yesterday the contours and points were all placed in a single marker set so objects could not be distinguished (except by color). Also noticed that yesterday's changes didn't make it to the web site because I copied a file to the wrong place. The latest IMOD file reader code is on the Chimera experimental features web page. Tom
participants (3)
-
David G. Morgan -
Tom Goddard -
William Jeffrey Triffo