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: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html 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. Tom -------- Original Message -------- Subject: Re: [Chimera-users] capping surface with a VRML model From: Damien Larivière <damien.lariviere@fourmentinguilbert.org> To: Thomas Goddard <goddard@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 :

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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

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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