measuring rotation between two homologous PDB models
Hi Elaine and ChimeraX Team
My query relates to measuring rotation between two subunits from homologous models in ChimeraX.
Here, I have first aligned the two models on one of sub-domains of these multi-domain complex. Then, without moving the models, the plan is to calculate the rotation in another domain, between the 2 models, apart from measuring the translational shift. So,
* Align Chain /L,M (model #1, PDB:6g2j ) and Chains /5,4 (model #2, PDB:6rfr). * Calculate rotation of Chain /F (model #1, PDB:6g2j) and Chain /B (model #2, PDB:6rfr).
I am using the following commands: -- open 6g2j; open 6rfr; -- match #1/L,N to #2/5,4 pair ss; -- measure rotation #1/F toModel #2/B coordinateSystem #1/F showAxis true showSlabs true;
The log report is: Position of 6g2j #1 relative to 6rfr #2 in 6g2j #1 coordinate system: Matrix rotation and translation 0.80441124 0.40360431 -0.43591986 67.76279700 0.18783349 0.52334489 0.83116106 -121.82969657 0.56359661 -0.75047565 0.34517410 202.31442783 Axis -0.83978100 -0.53070022 -0.11456502 Axis point 0.00000000 87.13355460 206.39866592 Rotation angle (degrees) 70.33834463 Shift along axis -15.42901832
Thus, ChimeraX is calculating a rotation of ¬70 degrees, which is clearly the case. The visual inspection suggests, that the rotation should be no more than ~15-20 degrees. I am not sure where I am going wrong. Could you please help?
Thanks Yaikhomba
Hi Yaikhomba, Measure rotation is simply telling you how #1 was already moved when it was matched to #2. It does NOT tell you the transformation between the domains in the after-matched position that would be needed to superimpose those domains. I tried to explain this in the help, but I know it's confusing:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation
If I understand correctly here is how I might try to do it:
(1) superimpose 6gj2 onto 6rfr like you did already (2) save PDB 6gj2 relative to 6rfr (in matched position) (3) close 6gj2 (4) reopen saved version of 6gj2 that is already matched on 6rfr (5) then superimpose those domains (6) then measure rotation
E.g. commands something like this:
open 6g2j; open 6rfr match #1/L,N to #2/5,4 pair ss save 6g2jnew.pdb #1 rel #2 close #1 open 6g2jnew.pdb match #1/F to #2/B measure rotation #1 to #2 coordinate #1 showAxis true showSlabs true
That gives a rotation of about 18 degrees, so maybe it is the measurement you had in mind. 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 26, 2021, at 8:41 AM, Y. Mutum via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine and ChimeraX Team
My query relates to measuring rotation between two subunits from homologous models in ChimeraX.
Here, I have first aligned the two models on one of sub-domains of these multi-domain complex. Then, without moving the models, the plan is to calculate the rotation in another domain, between the 2 models, apart from measuring the translational shift. So, • Align Chain /L,M (model #1, PDB:6g2j ) and Chains /5,4 (model #2, PDB:6rfr). • Calculate rotation of Chain /F (model #1, PDB:6g2j) and Chain /B (model #2, PDB:6rfr). I am using the following commands: -- open 6g2j; open 6rfr; -- match #1/L,N to #2/5,4 pair ss; -- measure rotation #1/F toModel #2/B coordinateSystem #1/F showAxis true showSlabs true;
The log report is: Position of 6g2j #1 relative to 6rfr #2 in 6g2j #1 coordinate system: Matrix rotation and translation 0.80441124 0.40360431 -0.43591986 67.76279700 0.18783349 0.52334489 0.83116106 -121.82969657 0.56359661 -0.75047565 0.34517410 202.31442783 Axis -0.83978100 -0.53070022 -0.11456502 Axis point 0.00000000 87.13355460 206.39866592 Rotation angle (degrees) 70.33834463 Shift along axis -15.42901832
Thus, ChimeraX is calculating a rotation of ¬70 degrees, which is clearly the case. The visual inspection suggests, that the rotation should be no more than ~15-20 degrees. I am not sure where I am going wrong. Could you please help?
Thanks Yaikhomba
Thank you Elaine. This helps.
________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: 26 November 2021 17:15 To: Y. Mutum ym337@cam.ac.uk Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] measuring rotation between two homologous PDB models
Hi Yaikhomba, Measure rotation is simply telling you how #1 was already moved when it was matched to #2. It does NOT tell you the transformation between the domains in the after-matched position that would be needed to superimpose those domains. I tried to explain this in the help, but I know it's confusing:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation
If I understand correctly here is how I might try to do it:
(1) superimpose 6gj2 onto 6rfr like you did already (2) save PDB 6gj2 relative to 6rfr (in matched position) (3) close 6gj2 (4) reopen saved version of 6gj2 that is already matched on 6rfr (5) then superimpose those domains (6) then measure rotation
E.g. commands something like this:
open 6g2j; open 6rfr match #1/L,N to #2/5,4 pair ss save 6g2jnew.pdb #1 rel #2 close #1 open 6g2jnew.pdb match #1/F to #2/B measure rotation #1 to #2 coordinate #1 showAxis true showSlabs true
That gives a rotation of about 18 degrees, so maybe it is the measurement you had in mind. 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 26, 2021, at 8:41 AM, Y. Mutum via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine and ChimeraX Team
My query relates to measuring rotation between two subunits from homologous models in ChimeraX.
Here, I have first aligned the two models on one of sub-domains of these multi-domain complex. Then, without moving the models, the plan is to calculate the rotation in another domain, between the 2 models, apart from measuring the translational shift. So, • Align Chain /L,M (model #1, PDB:6g2j ) and Chains /5,4 (model #2, PDB:6rfr). • Calculate rotation of Chain /F (model #1, PDB:6g2j) and Chain /B (model #2, PDB:6rfr). I am using the following commands: -- open 6g2j; open 6rfr; -- match #1/L,N to #2/5,4 pair ss; -- measure rotation #1/F toModel #2/B coordinateSystem #1/F showAxis true showSlabs true;
The log report is: Position of 6g2j #1 relative to 6rfr #2 in 6g2j #1 coordinate system: Matrix rotation and translation 0.80441124 0.40360431 -0.43591986 67.76279700 0.18783349 0.52334489 0.83116106 -121.82969657 0.56359661 -0.75047565 0.34517410 202.31442783 Axis -0.83978100 -0.53070022 -0.11456502 Axis point 0.00000000 87.13355460 206.39866592 Rotation angle (degrees) 70.33834463 Shift along axis -15.42901832
Thus, ChimeraX is calculating a rotation of ¬70 degrees, which is clearly the case. The visual inspection suggests, that the rotation should be no more than ~15-20 degrees. I am not sure where I am going wrong. Could you please help?
Thanks Yaikhomba
Oh this is an excellent tool. Thank you Yaikhomba!
Dr. Meng,
Is there anyway, to change the size of the wedges using the same example.
Thank you again and have a great day Kako
----- Original Message -----
From: Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu To: "Y. Mutum" ym337@cam.ac.uk Cc: "chimerax-users@cgl.ucsf.edu" chimerax-users@cgl.ucsf.edu Date: 2021-11-27 02:15:46 Subject: Re: [chimerax-users] measuring rotation between two homologous PDB models
Hi Yaikhomba, Measure rotation is simply telling you how #1 was already moved when it was matched to #2. It does NOT tell you the transformation between the domains in the after-matched position that would be needed to superimpose those domains. I tried to explain this in the help, but I know it's confusing:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation
If I understand correctly here is how I might try to do it:
(1) superimpose 6gj2 onto 6rfr like you did already (2) save PDB 6gj2 relative to 6rfr (in matched position) (3) close 6gj2 (4) reopen saved version of 6gj2 that is already matched on 6rfr (5) then superimpose those domains (6) then measure rotation
E.g. commands something like this:
open 6g2j; open 6rfr match #1/L,N to #2/5,4 pair ss save 6g2jnew.pdb #1 rel #2 close #1 open 6g2jnew.pdb match #1/F to #2/B measure rotation #1 to #2 coordinate #1 showAxis true showSlabs true
That gives a rotation of about 18 degrees, so maybe it is the measurement you had in mind. 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 26, 2021, at 8:41 AM, Y. Mutum via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine and ChimeraX Team
My query relates to measuring rotation between two subunits from homologous models in ChimeraX.
Here, I have first aligned the two models on one of sub-domains of these multi-domain complex. Then, without moving the models, the plan is to calculate the rotation in another domain, between the 2 models, apart from measuring the translational shift. So, • Align Chain /L,M (model #1, PDB:6g2j ) and Chains /5,4 (model #2, PDB:6rfr). • Calculate rotation of Chain /F (model #1, PDB:6g2j) and Chain /B (model #2, PDB:6rfr). I am using the following commands: -- open 6g2j; open 6rfr; -- match #1/L,N to #2/5,4 pair ss; -- measure rotation #1/F toModel #2/B coordinateSystem #1/F showAxis true showSlabs true;
The log report is: Position of 6g2j #1 relative to 6rfr #2 in 6g2j #1 coordinate system: Matrix rotation and translation 0.80441124 0.40360431 -0.43591986 67.76279700 0.18783349 0.52334489 0.83116106 -121.82969657 0.56359661 -0.75047565 0.34517410 202.31442783 Axis -0.83978100 -0.53070022 -0.11456502 Axis point 0.00000000 87.13355460 206.39866592 Rotation angle (degrees) 70.33834463 Shift along axis -15.42901832
Thus, ChimeraX is calculating a rotation of ¬70 degrees, which is clearly the case. The visual inspection suggests, that the rotation should be no more than ~15-20 degrees. I am not sure where I am going wrong. Could you please help?
Thanks Yaikhomba
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Kako, If you mean the rectangular slabs, yes, there are length, width, and height options. You can see the help (including what options are available and their default values) with command "help measure rotation", or see the copy at our website here:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 26, 2021, at 4:33 PM, Stapleton kevin2017/4/3 kevin.aug@protein.osaka-u.ac.jp wrote:
Oh this is an excellent tool. Thank you Yaikhomba!
Dr. Meng,
Is there anyway, to change the size of the wedges using the same example.
Thank you again and have a great day Kako
----- Original Message -----
From: Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu To: "Y. Mutum" ym337@cam.ac.uk Cc: "chimerax-users@cgl.ucsf.edu" chimerax-users@cgl.ucsf.edu Date: 2021-11-27 02:15:46 Subject: Re: [chimerax-users] measuring rotation between two homologous PDB models
Hi Yaikhomba, Measure rotation is simply telling you how #1 was already moved when it was matched to #2. It does NOT tell you the transformation between the domains in the after-matched position that would be needed to superimpose those domains. I tried to explain this in the help, but I know it's confusing:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation
If I understand correctly here is how I might try to do it:
(1) superimpose 6gj2 onto 6rfr like you did already (2) save PDB 6gj2 relative to 6rfr (in matched position) (3) close 6gj2 (4) reopen saved version of 6gj2 that is already matched on 6rfr (5) then superimpose those domains (6) then measure rotation
E.g. commands something like this:
open 6g2j; open 6rfr match #1/L,N to #2/5,4 pair ss save 6g2jnew.pdb #1 rel #2 close #1 open 6g2jnew.pdb match #1/F to #2/B measure rotation #1 to #2 coordinate #1 showAxis true showSlabs true
That gives a rotation of about 18 degrees, so maybe it is the measurement you had in mind. 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 26, 2021, at 8:41 AM, Y. Mutum via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine and ChimeraX Team
My query relates to measuring rotation between two subunits from homologous models in ChimeraX.
Here, I have first aligned the two models on one of sub-domains of these multi-domain complex. Then, without moving the models, the plan is to calculate the rotation in another domain, between the 2 models, apart from measuring the translational shift. So, • Align Chain /L,M (model #1, PDB:6g2j ) and Chains /5,4 (model #2, PDB:6rfr). • Calculate rotation of Chain /F (model #1, PDB:6g2j) and Chain /B (model #2, PDB:6rfr). I am using the following commands: -- open 6g2j; open 6rfr; -- match #1/L,N to #2/5,4 pair ss; -- measure rotation #1/F toModel #2/B coordinateSystem #1/F showAxis true showSlabs true;
The log report is: Position of 6g2j #1 relative to 6rfr #2 in 6g2j #1 coordinate system: Matrix rotation and translation 0.80441124 0.40360431 -0.43591986 67.76279700 0.18783349 0.52334489 0.83116106 -121.82969657 0.56359661 -0.75047565 0.34517410 202.31442783 Axis -0.83978100 -0.53070022 -0.11456502 Axis point 0.00000000 87.13355460 206.39866592 Rotation angle (degrees) 70.33834463 Shift along axis -15.42901832
Thus, ChimeraX is calculating a rotation of ¬70 degrees, which is clearly the case. The visual inspection suggests, that the rotation should be no more than ~15-20 degrees. I am not sure where I am going wrong. Could you please help?
Thanks Yaikhomba
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Awesome! Thanks again for all the help. Next time I will make sure to actually look at the link before emailing :-)
Have a great day KAko
----- Original Message -----
From: Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu To: Stapleton kevin2017/4/3 kevin.aug@protein.osaka-u.ac.jp Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu,"Y. Mutum" ym337@cam.ac.uk Date: 2021-11-27 09:59:23 Subject: Re: [chimerax-users] measuring rotation between two homologous PDB models
Hi Kako, If you mean the rectangular slabs, yes, there are length, width, and height options. You can see the help (including what options are available and their default values) with command "help measure rotation", or see the copy at our website here:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 26, 2021, at 4:33 PM, Stapleton kevin2017/4/3 kevin.aug@protein.osaka-u.ac.jp wrote:
Oh this is an excellent tool. Thank you Yaikhomba!
Dr. Meng,
Is there anyway, to change the size of the wedges using the same example.
Thank you again and have a great day Kako
----- Original Message -----
From: Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu To: "Y. Mutum" ym337@cam.ac.uk Cc: "chimerax-users@cgl.ucsf.edu" chimerax-users@cgl.ucsf.edu Date: 2021-11-27 02:15:46 Subject: Re: [chimerax-users] measuring rotation between two homologous PDB models
Hi Yaikhomba, Measure rotation is simply telling you how #1 was already moved when it was matched to #2. It does NOT tell you the transformation between the domains in the after-matched position that would be needed to superimpose those domains. I tried to explain this in the help, but I know it's confusing:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation
If I understand correctly here is how I might try to do it:
(1) superimpose 6gj2 onto 6rfr like you did already (2) save PDB 6gj2 relative to 6rfr (in matched position) (3) close 6gj2 (4) reopen saved version of 6gj2 that is already matched on 6rfr (5) then superimpose those domains (6) then measure rotation
E.g. commands something like this:
open 6g2j; open 6rfr match #1/L,N to #2/5,4 pair ss save 6g2jnew.pdb #1 rel #2 close #1 open 6g2jnew.pdb match #1/F to #2/B measure rotation #1 to #2 coordinate #1 showAxis true showSlabs true
That gives a rotation of about 18 degrees, so maybe it is the measurement you had in mind. 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 26, 2021, at 8:41 AM, Y. Mutum via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine and ChimeraX Team
My query relates to measuring rotation between two subunits from homologous models in ChimeraX.
Here, I have first aligned the two models on one of sub-domains of these multi-domain complex. Then, without moving the models, the plan is to calculate the rotation in another domain, between the 2 models, apart from measuring the translational shift. So, • Align Chain /L,M (model #1, PDB:6g2j ) and Chains /5,4 (model #2, PDB:6rfr). • Calculate rotation of Chain /F (model #1, PDB:6g2j) and Chain /B (model #2, PDB:6rfr). I am using the following commands: -- open 6g2j; open 6rfr; -- match #1/L,N to #2/5,4 pair ss; -- measure rotation #1/F toModel #2/B coordinateSystem #1/F showAxis true showSlabs true;
The log report is: Position of 6g2j #1 relative to 6rfr #2 in 6g2j #1 coordinate system: Matrix rotation and translation 0.80441124 0.40360431 -0.43591986 67.76279700 0.18783349 0.52334489 0.83116106 -121.82969657 0.56359661 -0.75047565 0.34517410 202.31442783 Axis -0.83978100 -0.53070022 -0.11456502 Axis point 0.00000000 87.13355460 206.39866592 Rotation angle (degrees) 70.33834463 Shift along axis -15.42901832
Thus, ChimeraX is calculating a rotation of ¬70 degrees, which is clearly the case. The visual inspection suggests, that the rotation should be no more than ~15-20 degrees. I am not sure where I am going wrong. Could you please help?
Thanks Yaikhomba
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Elaine Meng -
Stapleton kevin2017/4/3 -
Y. Mutum