ChimeraX import multiple positions of the same .pdb structure
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
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
Hi Lukas, Did you try simply omitting "childModels true" when opening the positions file? As I understand it, if you omit it (childModels defaults to false) then the matrix for #1 will apply to all of #1 including its submodels, but when you set "childModels true," then the positions file is expected to contain a matrix for each submodel as well... which it does not.
However, if that does not work either, let us know. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 23, 2021, at 2:51 PM, Frey, Lukas via ChimeraX-users chimerax-users@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
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
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@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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participants (3)
-
Elaine Meng -
Frey, Lukas -
Tom Goddard