Dear chimeras users and developers, I would like to translate and rotate a model according to the rotation and translation matrix given by a fitmap. More precisely : I fit model #2 in map #1 and save the corresponding translation and rotation matrix with the save command. Then, I want to turn and move a model #3 so that it has the same position and rotation as model #2 (each correspond to the same pdb file). However, I want to do this automatically, so I need to do it from the matrix that is saved in a .positions file, and not from the (axis, axis point, rotation angle and shift along axis) values given by fitmap, but from the Matrix rotation and translation values. So far, - I compute the axis of rotation and the angle from the rotation matrix given by fitmap models #2 inMap #1 - I turn #3 around this axis and angle, in coordinateSystems #1 - I apply the translation also measured by fitmap models #2 inMap #1 to #3 (with three calls of the move command, for each axis x,y,z) However, there is a small gap between model #2 and model #3, whereas both should be at the exact same position. Maybe this has to do with the rotation center that is used in fitMap, but it cannot be saved in a .positions file, and I don't know how to recover it from the matrix rotation and translation given by fitmap. Do you have any idea of what I'm doing wrong, or how I could place model #3 at the same exact position as model #2 from the .positions file of model #2, and by moving and rotating model #3 ? (What I want to do then is re-apply this same transformation to build a chain of the same protein) Thanks, Lar Lara KOEHLER Laboratoire de Physique Théorique et Modèles Statistiques Bureau L123 - Bâtiment 530 - Rue André Rivière 91400 Orsay [ http://www.universite-paris-saclay.fr/ | www.universite-paris-saclay.fr ]
Dear Lara, If I understand correctly, it is not necessary to use such an elaborate procedure or to save a positions file. Instead you could just use the "view position" command to apply the rotation/translation of one model to another model, something like: view position #3 sameas #2 See: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#position> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 9, 2020, at 10:48 AM, Lara Koehler <lara.koehler@universite-paris-saclay.fr> wrote:
Dear chimeras users and developers,
I would like to translate and rotate a model according to the rotation and translation matrix given by a fitmap. More precisely : I fit model #2 in map #1 and save the corresponding translation and rotation matrix with the save command. Then, I want to turn and move a model #3 so that it has the same position and rotation as model #2 (each correspond to the same pdb file). However, I want to do this automatically, so I need to do it from the matrix that is saved in a .positions file, and not from the (axis, axis point, rotation angle and shift along axis) values given by fitmap, but from the Matrix rotation and translation values. So far, - I compute the axis of rotation and the angle from the rotation matrix given by fitmap models #2 inMap #1 - I turn #3 around this axis and angle, in coordinateSystems #1 - I apply the translation also measured by fitmap models #2 inMap #1 to #3 (with three calls of the move command, for each axis x,y,z) However, there is a small gap between model #2 and model #3, whereas both should be at the exact same position.
Maybe this has to do with the rotation center that is used in fitMap, but it cannot be saved in a .positions file, and I don't know how to recover it from the matrix rotation and translation given by fitmap. Do you have any idea of what I'm doing wrong, or how I could place model #3 at the same exact position as model #2 from the .positions file of model #2, and by moving and rotating model #3 ? (What I want to do then is re-apply this same transformation to build a chain of the same protein) Thanks, Lar
Note that repeated use of "view position" would just put the protein copies all in the same place as each other, not make a chain. To make a chain, you would need two copies already placed in the proper relationship *relative* to one another (say B to A), measure that relative transformation, and then apply it to subsequent copies (C to B, D to C, ...) If A and B are just copies of the same input file, I believe that "measure rotation" would give you the relative transformation. See: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation> However, I'm not sure how you would apply that relative transformation to additional copies. It might require some matrix math. Elaine
On Dec 9, 2020, at 11:15 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Lara, If I understand correctly, it is not necessary to use such an elaborate procedure or to save a positions file. Instead you could just use the "view position" command to apply the rotation/translation of one model to another model, something like:
view position #3 sameas #2
See: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#position>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 9, 2020, at 10:48 AM, Lara Koehler <lara.koehler@universite-paris-saclay.fr> wrote:
Dear chimeras users and developers,
I would like to translate and rotate a model according to the rotation and translation matrix given by a fitmap. More precisely : I fit model #2 in map #1 and save the corresponding translation and rotation matrix with the save command. Then, I want to turn and move a model #3 so that it has the same position and rotation as model #2 (each correspond to the same pdb file). However, I want to do this automatically, so I need to do it from the matrix that is saved in a .positions file, and not from the (axis, axis point, rotation angle and shift along axis) values given by fitmap, but from the Matrix rotation and translation values. So far, - I compute the axis of rotation and the angle from the rotation matrix given by fitmap models #2 inMap #1 - I turn #3 around this axis and angle, in coordinateSystems #1 - I apply the translation also measured by fitmap models #2 inMap #1 to #3 (with three calls of the move command, for each axis x,y,z) However, there is a small gap between model #2 and model #3, whereas both should be at the exact same position.
Maybe this has to do with the rotation center that is used in fitMap, but it cannot be saved in a .positions file, and I don't know how to recover it from the matrix rotation and translation given by fitmap. Do you have any idea of what I'm doing wrong, or how I could place model #3 at the same exact position as model #2 from the .positions file of model #2, and by moving and rotating model #3 ? (What I want to do then is re-apply this same transformation to build a chain of the same protein) Thanks, Lar
Hi Elaine, Thanks a lot for your answer. This repetition of relative motion is exactly what I intend to do. What I am planning to do is generate a command .cxc file automatically, through a python loop for example. But before, I need to check that I am correctly positioning B with respect to A (so that I can then repeat the operation). But when I do that with the procedure I have described below (positioning B with respect to A with a fit on the one hand, and B' with respect to A with "move" and "turns" with values computed from "matrix rotation and translation" on the other end), I don't find the same result, and there is a tiny mismatch between B and B'. "measure rotation" gives me the same matrix as "fitmap", yet what I can save in a .positions file to generate this transformation several time is only the matrix rotation and translation. Do you understand my problem ? Lara De: "Elaine Meng" <meng@cgl.ucsf.edu> À: "Lara Koehler" <lara.koehler@universite-paris-saclay.fr> Cc: "ChimeraX Users Help" <chimerax-users@cgl.ucsf.edu> Envoyé: Mercredi 9 Décembre 2020 20:26:44 Objet: Re: [chimerax-users] Move model from position Note that repeated use of "view position" would just put the protein copies all in the same place as each other, not make a chain. To make a chain, you would need two copies already placed in the proper relationship *relative* to one another (say B to A), measure that relative transformation, and then apply it to subsequent copies (C to B, D to C, ...) If A and B are just copies of the same input file, I believe that "measure rotation" would give you the relative transformation. See: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation> However, I'm not sure how you would apply that relative transformation to additional copies. It might require some matrix math. Elaine
On Dec 9, 2020, at 11:15 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Lara, If I understand correctly, it is not necessary to use such an elaborate procedure or to save a positions file. Instead you could just use the "view position" command to apply the rotation/translation of one model to another model, something like:
view position #3 sameas #2
See: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#position>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 9, 2020, at 10:48 AM, Lara Koehler <lara.koehler@universite-paris-saclay.fr> wrote:
Dear chimeras users and developers,
I would like to translate and rotate a model according to the rotation and translation matrix given by a fitmap. More precisely : I fit model #2 in map #1 and save the corresponding translation and rotation matrix with the save command. Then, I want to turn and move a model #3 so that it has the same position and rotation as model #2 (each correspond to the same pdb file). However, I want to do this automatically, so I need to do it from the matrix that is saved in a .positions file, and not from the (axis, axis point, rotation angle and shift along axis) values given by fitmap, but from the Matrix rotation and translation values. So far, - I compute the axis of rotation and the angle from the rotation matrix given by fitmap models #2 inMap #1 - I turn #3 around this axis and angle, in coordinateSystems #1 - I apply the translation also measured by fitmap models #2 inMap #1 to #3 (with three calls of the move command, for each axis x,y,z) However, there is a small gap between model #2 and model #3, whereas both should be at the exact same position.
Maybe this has to do with the rotation center that is used in fitMap, but it cannot be saved in a .positions file, and I don't know how to recover it from the matrix rotation and translation given by fitmap. Do you have any idea of what I'm doing wrong, or how I could place model #3 at the same exact position as model #2 from the .positions file of model #2, and by moving and rotating model #3 ? (What I want to do then is re-apply this same transformation to build a chain of the same protein) Thanks, Lar
Hi Lara, It may be rounding issues that cause the small differences. Instead of "move" and "turn" you can use "view matrix" to apply a matrix, but I don't know if that will prevent getting small differences. See: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix> Elaine
On Dec 9, 2020, at 11:42 AM, Lara Koehler <lara.koehler@universite-paris-saclay.fr> wrote:
Hi Elaine, Thanks a lot for your answer. This repetition of relative motion is exactly what I intend to do. What I am planning to do is generate a command .cxc file automatically, through a python loop for example. But before, I need to check that I am correctly positioning B with respect to A (so that I can then repeat the operation). But when I do that with the procedure I have described below (positioning B with respect to A with a fit on the one hand, and B' with respect to A with "move" and "turns" with values computed from "matrix rotation and translation" on the other end), I don't find the same result, and there is a tiny mismatch between B and B'. "measure rotation" gives me the same matrix as "fitmap", yet what I can save in a .positions file to generate this transformation several time is only the matrix rotation and translation. Do you understand my problem ?
Lara
De: "Elaine Meng" <meng@cgl.ucsf.edu> À: "Lara Koehler" <lara.koehler@universite-paris-saclay.fr> Cc: "ChimeraX Users Help" <chimerax-users@cgl.ucsf.edu> Envoyé: Mercredi 9 Décembre 2020 20:26:44 Objet: Re: [chimerax-users] Move model from position
Note that repeated use of "view position" would just put the protein copies all in the same place as each other, not make a chain. To make a chain, you would need two copies already placed in the proper relationship *relative* to one another (say B to A), measure that relative transformation, and then apply it to subsequent copies (C to B, D to C, ...)
If A and B are just copies of the same input file, I believe that "measure rotation" would give you the relative transformation. See: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>
However, I'm not sure how you would apply that relative transformation to additional copies. It might require some matrix math.
Elaine
On Dec 9, 2020, at 11:15 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Lara, If I understand correctly, it is not necessary to use such an elaborate procedure or to save a positions file. Instead you could just use the "view position" command to apply the rotation/translation of one model to another model, something like:
view position #3 sameas #2
See: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#position>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 9, 2020, at 10:48 AM, Lara Koehler <lara.koehler@universite-paris-saclay.fr> wrote:
Dear chimeras users and developers,
I would like to translate and rotate a model according to the rotation and translation matrix given by a fitmap. More precisely : I fit model #2 in map #1 and save the corresponding translation and rotation matrix with the save command. Then, I want to turn and move a model #3 so that it has the same position and rotation as model #2 (each correspond to the same pdb file). However, I want to do this automatically, so I need to do it from the matrix that is saved in a .positions file, and not from the (axis, axis point, rotation angle and shift along axis) values given by fitmap, but from the Matrix rotation and translation values. So far, - I compute the axis of rotation and the angle from the rotation matrix given by fitmap models #2 inMap #1 - I turn #3 around this axis and angle, in coordinateSystems #1 - I apply the translation also measured by fitmap models #2 inMap #1 to #3 (with three calls of the move command, for each axis x,y,z) However, there is a small gap between model #2 and model #3, whereas both should be at the exact same position.
Maybe this has to do with the rotation center that is used in fitMap, but it cannot be saved in a .positions file, and I don't know how to recover it from the matrix rotation and translation given by fitmap. Do you have any idea of what I'm doing wrong, or how I could place model #3 at the same exact position as model #2 from the .positions file of model #2, and by moving and rotating model #3 ? (What I want to do then is re-apply this same transformation to build a chain of the same protein) Thanks, Lar
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Hi Elaine, This solved my problem, thanks a lot ! Lara De: "Elaine Meng" <meng@cgl.ucsf.edu> À: "Lara Koehler" <lara.koehler@universite-paris-saclay.fr> Cc: "ChimeraX Users Help" <chimerax-users@cgl.ucsf.edu> Envoyé: Mercredi 9 Décembre 2020 20:51:40 Objet: Re: [chimerax-users] Move model from position Hi Lara, It may be rounding issues that cause the small differences. Instead of "move" and "turn" you can use "view matrix" to apply a matrix, but I don't know if that will prevent getting small differences. See: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix> Elaine
On Dec 9, 2020, at 11:42 AM, Lara Koehler <lara.koehler@universite-paris-saclay.fr> wrote:
Hi Elaine, Thanks a lot for your answer. This repetition of relative motion is exactly what I intend to do. What I am planning to do is generate a command .cxc file automatically, through a python loop for example. But before, I need to check that I am correctly positioning B with respect to A (so that I can then repeat the operation). But when I do that with the procedure I have described below (positioning B with respect to A with a fit on the one hand, and B' with respect to A with "move" and "turns" with values computed from "matrix rotation and translation" on the other end), I don't find the same result, and there is a tiny mismatch between B and B'. "measure rotation" gives me the same matrix as "fitmap", yet what I can save in a .positions file to generate this transformation several time is only the matrix rotation and translation. Do you understand my problem ?
Lara
De: "Elaine Meng" <meng@cgl.ucsf.edu> À: "Lara Koehler" <lara.koehler@universite-paris-saclay.fr> Cc: "ChimeraX Users Help" <chimerax-users@cgl.ucsf.edu> Envoyé: Mercredi 9 Décembre 2020 20:26:44 Objet: Re: [chimerax-users] Move model from position
Note that repeated use of "view position" would just put the protein copies all in the same place as each other, not make a chain. To make a chain, you would need two copies already placed in the proper relationship *relative* to one another (say B to A), measure that relative transformation, and then apply it to subsequent copies (C to B, D to C, ...)
If A and B are just copies of the same input file, I believe that "measure rotation" would give you the relative transformation. See: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>
However, I'm not sure how you would apply that relative transformation to additional copies. It might require some matrix math.
Elaine
On Dec 9, 2020, at 11:15 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Lara, If I understand correctly, it is not necessary to use such an elaborate procedure or to save a positions file. Instead you could just use the "view position" command to apply the rotation/translation of one model to another model, something like:
view position #3 sameas #2
See: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#position>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 9, 2020, at 10:48 AM, Lara Koehler <lara.koehler@universite-paris-saclay.fr> wrote:
Dear chimeras users and developers,
I would like to translate and rotate a model according to the rotation and translation matrix given by a fitmap. More precisely : I fit model #2 in map #1 and save the corresponding translation and rotation matrix with the save command. Then, I want to turn and move a model #3 so that it has the same position and rotation as model #2 (each correspond to the same pdb file). However, I want to do this automatically, so I need to do it from the matrix that is saved in a .positions file, and not from the (axis, axis point, rotation angle and shift along axis) values given by fitmap, but from the Matrix rotation and translation values. So far, - I compute the axis of rotation and the angle from the rotation matrix given by fitmap models #2 inMap #1 - I turn #3 around this axis and angle, in coordinateSystems #1 - I apply the translation also measured by fitmap models #2 inMap #1 to #3 (with three calls of the move command, for each axis x,y,z) However, there is a small gap between model #2 and model #3, whereas both should be at the exact same position.
Maybe this has to do with the rotation center that is used in fitMap, but it cannot be saved in a .positions file, and I don't know how to recover it from the matrix rotation and translation given by fitmap. Do you have any idea of what I'm doing wrong, or how I could place model #3 at the same exact position as model #2 from the .positions file of model #2, and by moving and rotating model #3 ? (What I want to do then is re-apply this same transformation to build a chain of the same protein) Thanks, Lar
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participants (2)
-
Elaine Meng -
Lara Koehler