[Chimera-users] Select multiscale model surface pieces with command lines

Tom Goddard goddard at sonic.net
Mon May 18 11:18:40 PDT 2015

Hi Tubiana,

  Unfortunately Chimera session do not remember selections of multiscale surfaces (or any other surfaces except solvent excluded molecular surfaces).  I’ve improved Chimera so that you can specify of multiscale surface in a command like “color red #1:5.A”.  The “5.A” part is the name of one of the individual surfaces in a multiscale model and I found that name by hovering the mouse of the surface I wanted.  This was from a virus capsid example (2bbv) with 3 chains A,B,C and the surfaces get named 1.A, 1.B, 1.C, 2.A, …., 60.A, 60.B, 60.C for the 60-fold icosahedral symmetry.  The code I added is limited and can only handle specifying one surface, e.g. it will not work to say “color red #1:5.A,5.B” but you could handle that for now by using two commands.  We are working on Chimera 2 so I don’t have a lot of time to fix Chimera 1 limitations.  I’m not sure what you want to do with the multiscale model in your movie.  There are few commands that you can use to manipulate those surfaces.  You can hide them with “sop hidePiece #1:5.A” show them with “sop showPiece #1:5.A”, or change their transparency “transp 50 #1:5.A”.

  The ability to specify a surface piece will be in tonight’s Chimera daily build.


> On May 17, 2015, at 2:09 AM, TUBIANA Thibault CNRS  wrote:
> Hi everyone!
> I Want to script a movie, but to do so, I need to select some surface pieces of a virus multiscale model with command line.
> I didn't find any way to do that. I try to select them with the mouse (ctrl+click) and then rename the selection with "namesel", it works but when I save the session and reload it, theses selections are cleared....
> I can't do that each times I load my session because I have plenty of them and it's to generate the movie on SSH on another computer more powerfull...
> I can't split them to create a new model (for exemple with coordinates) because I will have to update all my "savepos" position...
> Did someone know how to do that ? 
> Thank you a lot for your help,
> Regards,
> --
> Tubiana Thibault
> PhD Student
> Institut de Biologie Intégrative de la Cellule 
> CNRS UMR 9198
> CEA-Saclay, Bâtiment 532 - Pce 12A
> 91191 Gif-sur-Yvette
> http://www.tubiana.me <http://www.tubiana.me/>_______________________________________________
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