[Chimera-users] Using Transformation matrix in Chimera

Tom Goddard goddard at sonic.net
Thu Apr 16 17:32:29 PDT 2020

Hi Ilan,

  I'm a bit puzzled by what you are trying to do.  It sounds like you are trying to make one map align with a PDB and then move several other maps that were aligned with that first map by the same transformation that aligned the first map.

  I think the simple approach is to eliminate steps 2 and 3.

  You start with your PDB and some reference map covering the PDB whose grid you will resample the maps on.  Now fitmap your PDB to the first target map.  Then move the reference grid to the same position as the fit PDB using the matrixcopy command to copy the PDB's position matrix to the grid map.  Now just resample your first target and all the others on this reference grid and save them.  If you then quit Chimera, restart, load the PDB and the new maps, the first target will be aligned with the PDB and the other targets will be moved by the same amount to align with the PDB.



> On Apr 16, 2020, at 4:12 PM, Chemmama, Ilan <Ilan.Chemmama at ucsf.edu> wrote:
> Dear Developers, 
> I have a set of maps that I am trying to transform the following way:
> i) Compute the transformation between a PDB and one of maps. 
> This is trivial using fitmap command. 
> ii) I would like to get the inverse transformation moving the PDB to its original position.
> I have tried to play with matrixget and matrixes but without much success in access the the inverse transformation.
> iii) Apply the inverse transformation to each of the map.
> I assume you can easily do that with move passing the inverse matrix obtained above with a little for loop on model #. 
> iv) Save the rotated maps
> This is trivial using vop resample and volume save.
> As you may see, I am struggling with step 2. Is there an easy way to access that matrix, get the inverse, and apply to a set of models. 
> I have tried to find a solution in both Chimera (using runCommand) and ChimeraX (using run from core.commands) but to no avail. 
> Any tips would be appreciated here - 
> Ilan
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