[chimerax-users] ChimeraX import multiple positions of the same .pdb structure

[Tom Goddard]

Hi Lukas,

  You matrix values are in the wrong order.  As it says in the documentation for "view matrix"

"Each matrix is reported as 12 comma-separated numbers, corresponding to a 3x3 rotation matrix and a translation vector in the fourth column. Ordering is row-by-row, such that the translation vector is given as the fourth, eighth, and twelfth numbers."

https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html#matrix <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html#matrix>

You instead have the translation as the tenth, eleventh and twelfth values.  This is why your models are skewed.

	Tom



> On Nov 23, 2021, at 2:51 PM, Frey, Lukas via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear Elaine,
> 
> I have an external file with a transformation matrix (orientation and translation) for a .pdb structure and I would like to apply the transformation in ChimeraX to a .pdb file. I’m aware that ChimeraX needs a matrix like  [[1,1,1],[2,2,2],[3,3,3],[x,y,z]], where the first 3 columns are the orientation the last column the x,y,z translation positions. One can load a new orientation/translation into chimeraX with the „open“ command:
> 
> https://rbvi.ucsf.edu/chimerax/docs/user/formats/positions.html <https://rbvi.ucsf.edu/chimerax/docs/user/formats/positions.html>
> 
> in the command line of chimeraX I had to type in:
> 
> open path-to-file/test.positions models #1 childModels true matchNames true 
> 
> my test.positions file is a .txt file containing the name of the .pdb structure and transformation matrix and I already loaded the .pdb structure before I applied the transformation matrix. Below you can find the input of the transformation matrix file, called text.positions:
> 
> 6y2l.pdb,-0.6515591636522021,-0.6041757901381976,-0.45873987277293393,0.09148867345316551,-0.662890582358989,0.7431055769199559,-0.7530607405054541,0.44220774578318395,0.48718767500700594,30.0,20.0,30.0
> 
> If I apply the open command in chimera somehow it leads to a distortion of the .pdb protein structure. If I check the transformation position of the model with „view matrix“, then I have the following output:
> 
> view matrix
> camera position: 0.94464,-0.25925,-0.20113,-578.87,-0.29451,-0.94014,-0.17144,1242.4,-0.14464,0.22118,-0.96445,-8143.8
> model positions: #1,-0.65156,-0.60418,-0.45874,0.091489,-0.66289,0.74311,-0.75306,0.44221,0.48719,30,20,30,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0
> 
> Somehow the transformation matrix is only applied to  #1 but not to #1.1 and #1.2, do you have an idea what I have to change?
> 
> If I save the transformation matrix of the distorted .pdb structure via the save command: 
> 
> save path-to-file/test_2.positions models #1 childModels true
> 
> I have the following output:
> 6y2l.pdb,-0.651559163652,-0.604175790138,-0.458739872773,0.0914886734532,-0.662890582359,0.74310557692,-0.753060740505,0.442207745783,0.487187675007,30,20,30
> metal coordination bonds,1,0,0,0,0,1,0,0,0,0,1,0
> missing structure,1,0,0,0,0,1,0,0,0,0,1,0
> 
> The goal in the future is to load several positions (1 … 100) of the same .pdb structures.
> 
> 
> Best,
> 
> Lukas
> 
> 
> 
> 
> Lukas Frey
> Visiting Postdoctoral Associate
> UMASS Medical School Worcester
> Grigorieff Laboratory 
> 
> 
> 
> 
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