[Chimera-users] capping surface with a VRML model

Tom Goddard goddard at cgl.ucsf.edu
Wed Nov 18 09:07:36 PST 2009

Hi Damien,

  You can place many copies of ribosomes using the multiscale dialog if 
you add the positioning matrices to the ribosome PDB file using REMARK 
350 BIOMT records.  The rotations and translations are specified as a 3 
by 4 matrix that look like:

REMARK 350   BIOMT1   7  -0.866025 0.5           0    0
REMARK 350   BIOMT2   7  -0.5          -0.866025 0    0
REMARK 350   BIOMT3   7  0               0              1 145

The record gives the matrix number (7 in the example), 3 columns giving 
the rotation matrix, and the final column giving the translation 
(applied after rotation).  The "sym" command Chimera documentation has a 
more complete example at the bottom of the page:


If you put these remarks in the PDB and open it and use the Multiscale 
dialog with symmetry type "biological unit" that will use these BIOMT 
matrices and place all the copies.  You can perhaps generate the BIOMT 
remarks in Matlab and then insert them into the ribosome PDB file with a 
text editor.

I plan on improving the sym command so it can make the multiscale 
surfaces, and I can also add an option so it can read the matrices from 
a separate file so we avoid the step of modifying the PDB file.  It will 
be some time before I make those changes.


-------- Original Message --------
Subject: Re: [Chimera-users] capping surface with a VRML model
From: Damien Larivière <damien.lariviere at fourmentinguilbert.org>
To: Thomas Goddard <goddard at cgl.ucsf.edu>
Date: 11/18/09 8:45 AM
> Thank you very much Greg and Tom for your answers!
> About Tom's suggestion:
> I have used Matlab to generate position and orientation coordinates 
> (quaternions) for hundreds not superposing proteins (I am studying 
> ribosome density in bacteria). The Matlab output is a matrix that is 
> transformed into a file under the VRML format. In this VRML file, the 
> geometry is given by the ribosome multiscale model surface obtained in 
> Chimera and then the geometry is instantiated for all the ribosomes.
> So, I use Matlab to generate coordinates, Chimera for getting 
> isosurface geometry. I use then software like 3DSMax or Chimera again 
> to display the VRML file. The problem I face is that 3DSMax is very 
> long to open the file. The opening is almost instantaneous in Chimera 
> but as Greg confirmed it is not possible to clip and cap the VRML 
> isosurfaces.
> The best way to do is to write a Chimera script able to read the 
> coordinates matrix and to attribute a ribosome multiscale model 
> surface for all the points. Thus, I avoid the VRML step, I work only 
> in Chimera where I can clip and cap and render only a section of a 
> very crowded scene. But I do not know python. Do you think whether 
> such a script is easy to write?
> Damien
> Thomas Goddard a écrit :
>> Hi Damien,
>>   Chimera cannot cap clipped VRML surfaces. It also can't change the 
>> coloring or transparency of VRML surfaces. VRML surfaces are 
>> different from all other surfaces in Chimera.
>>   Why not just save the Chimera session with the multiscale model 
>> surface?  Then you can reopen it and clip and cap as you wish.
>>     Tom
>> -------- Original Message --------
>> Subject: [Chimera-users] capping surface with a VRML model
>> From: Damien Larivière
>> To: chimera-users
>> Date: 11/17/09 9:51 AM
>>> Dear all,
>>> It is possible in Chimera to cap the clipped surface of an 
>>> isosurface made with the Multiscale Model tool.
>>> However, if the isosurface is exported in VRML and then reopened in 
>>> Chimera, it is no more possible to cap the clipped surface. This 
>>> function (surface capping) is very interesting in particular when 
>>> the scene is crowded by many proteins. Is it a way to cap VRML model?
>>> Many thanks for your help!
>>> Damien

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