[Chimera-users] imod model viewing

[Tom Goddard]

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/CCDB_DATA_USER.portal/P1694/Experiment_3423/Subject_137/Tissue_155/Microscopy_3632/CTL_ImmunSynapse_seg.tar

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
>
> =============================================
>
>
>
>
> 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 at 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>
>