[Chimera-users] Chimera Multiscale using VRML?

[Thomas Goddard]

Hi Dong,

  The Chimera Multiscale extension is described in the Chimera User's Guide
in the Tools section.

	http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html

It currently calculates surfaces for PDB models and positions multiple
copies of those surfaces using matrices, like the BIOMT (biological
unit) matrices in PDB file headers.

  If I understand your question correctly, you want multiscale to use
your own VRML model for individual proteins instead of the surfaces it
normally calculates.  It won't do that, and it is not a simple change
to make.

  If you want a VRML model of a virus and you have the positioning matrices
and a VRML surface for one asymmetric unit, you could create a new VRML file
in an editor using the Transform VRML node to position each of the subunits.
But such a model would not be interactive like the Multiscale models -- you
would not be able to change to ribbon display, look at atomic contacts, ....

      Tom




>  Dear my concern
> 
> Thank you for the distribution of this nice program, Chimera!
> 
> Recently I downloaded new version of Chimera for Win32, 2056 build.
> 
> Most of all function is fine but when I tried to export surface as VRML, the
> button for "save" is not activated.
> 
> Instead of "save" there is "open" button. This button could be activated
> only by clicking "present file".
> 
> If user clicks that activated button, the original file has gone and
> replaced with new content's keeping its name.
> 
> Is there any way to export other model, like ribbon or space fill model as
> VRML?
> 
> I think it will be very helpful.
> 
> I tried lots of program, but the other programs are not good as Chimera at
> least in terms of VRML export.
> 
> My main purpose of using this program is "Multiscale modeling" ; I am so
> interested in virus capsid model.
> 
> It is so fabulous!!.
> 
> I have never seen this function before and I love this..
> 
> However is it possible to make multiscale model from other format like VRML?
> 
> I don't know exactly how chimera makes multiscale model, but I think chimera
> may use the matrix.
> 
> If then, I can guess we can make model from any format file whatever it is.
> 
> Would you help me how to do this work?
> 
> 
> And one more thing...
> 
> The exported surface file VRML format from chimera starts with
> 
> #VRML V2.0 utf8
> 
> Transform {
> 
> children [
> 
> Shape {
> 
> ....
> 
> And ended with ]}
> 
> 
> However without
> 
> 
> Transform {
> 
> Children [
> 
> 
> 
> ] }
> 
> Sentence there is no problem to view this file.
> 
> Moreover, some program which can import VRML file does not recognize
> original exported file.
> 
> After delete above sentence they could import VRML file.
> 
> 
> Thank you
> 
> 
> Dong Hoon Chung