Hi, I would like to calculate the rotation axis between two domains of a protein (domains are highly similar in fold and sequence). Is there a way to calculate transformation matrix between two objects in chimera (two domains here) to obtain the direction of rotation axis and rotation angle values? Also is it possible to generate a translation vector along rotation axis in graphic screen? Would be great if there is a script available for that and someone can share. Have a lovely weekend, arvind.
Hi Arvind, Here is one approach: (1) open the structure twice (as two models in Chimera, #0 and #1) (2) superimpose domain A of one model onto domain B of the other model, using whatever method you prefer (“match” command specifying the exact atoms to use, or “matchmaker” command or GUI which uses CA atoms only and figures out the residue pairing for you, or even by hand, although that is usually harder) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html> (3) use “measure rotation #0 #1” which will also display an axis (see options for axis color, slab display to show rotation and shift, etc.). Other things like shift and rotation angle are reported in the Log. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> (4) then you could hide or close one copy of the structure since it was only used to figure out this rotation I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 15, 2019, at 8:59 AM, Arvind SHARMA <arvind.sharma@pasteur.fr> wrote:
Hi, I would like to calculate the rotation axis between two domains of a protein (domains are highly similar in fold and sequence). Is there a way to calculate transformation matrix between two objects in chimera (two domains here) to obtain the direction of rotation axis and rotation angle values? Also is it possible to generate a translation vector along rotation axis in graphic screen? Would be great if there is a script available for that and someone can share.
Have a lovely weekend, arvind.
Hi Elaine, thanks a lot. Its perfect, exactly what I needed! Just one more question, is there a way to control the length and width of the rotation axis rod? best wishes, Arvind ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, March 15, 2019 5:48:36 PM To: Arvind SHARMA Cc: chimera List Subject: Re: [Chimera-users] drawing axes of rotational symmetry Hi Arvind, Here is one approach: (1) open the structure twice (as two models in Chimera, #0 and #1) (2) superimpose domain A of one model onto domain B of the other model, using whatever method you prefer (“match” command specifying the exact atoms to use, or “matchmaker” command or GUI which uses CA atoms only and figures out the residue pairing for you, or even by hand, although that is usually harder) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html> (3) use “measure rotation #0 #1” which will also display an axis (see options for axis color, slab display to show rotation and shift, etc.). Other things like shift and rotation angle are reported in the Log. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> (4) then you could hide or close one copy of the structure since it was only used to figure out this rotation I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 15, 2019, at 8:59 AM, Arvind SHARMA <arvind.sharma@pasteur.fr> wrote:
Hi, I would like to calculate the rotation axis between two domains of a protein (domains are highly similar in fold and sequence). Is there a way to calculate transformation matrix between two objects in chimera (two domains here) to obtain the direction of rotation axis and rotation angle values? Also is it possible to generate a translation vector along rotation axis in graphic screen? Would be great if there is a script available for that and someone can share.
Have a lovely weekend, arvind.
length: no width: not in the “measure rotation” command, but it’s essentially a stick bond between two fake atoms (markers), so you can use any of the same methods you could use to change stick bond thickness. For example, Ctrl-click the axis from “measure rotation" to select it and then open Selection Inspector (e.g. click green magnifying glass icon near lower right of window), inspect: bond, change radius. Then the markers on the ends will be bigger than the bond in between, but you could also select those markers (just like atoms, ctrl-click, Shift-ctrl-click) inspect: Atom, change radius to match the bond. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html> Or you could use the information in the Log to make your own 3D objects by defining them in a BILD-format file (simple text for cylinders, cones, etc.) and then opening that BILD file in Chimera. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html> I hope this helps, Elaine
On Mar 15, 2019, at 11:12 AM, Arvind SHARMA <arvind.sharma@pasteur.fr> wrote:
Hi Elaine,
thanks a lot. Its perfect, exactly what I needed! Just one more question, is there a way to control the length and width of the rotation axis rod?
best wishes, Arvind
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, March 15, 2019 5:48:36 PM To: Arvind SHARMA Cc: chimera List Subject: Re: [Chimera-users] drawing axes of rotational symmetry
Hi Arvind, Here is one approach:
(1) open the structure twice (as two models in Chimera, #0 and #1)
(2) superimpose domain A of one model onto domain B of the other model, using whatever method you prefer (“match” command specifying the exact atoms to use, or “matchmaker” command or GUI which uses CA atoms only and figures out the residue pairing for you, or even by hand, although that is usually harder)
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>
(3) use “measure rotation #0 #1” which will also display an axis (see options for axis color, slab display to show rotation and shift, etc.). Other things like shift and rotation angle are reported in the Log. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation>
(4) then you could hide or close one copy of the structure since it was only used to figure out this rotation
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 15, 2019, at 8:59 AM, Arvind SHARMA <arvind.sharma@pasteur.fr> wrote:
Hi, I would like to calculate the rotation axis between two domains of a protein (domains are highly similar in fold and sequence). Is there a way to calculate transformation matrix between two objects in chimera (two domains here) to obtain the direction of rotation axis and rotation angle values? Also is it possible to generate a translation vector along rotation axis in graphic screen? Would be great if there is a script available for that and someone can share.
Have a lovely weekend, arvind.
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
this was greatly helpful. thanks a lot Elaine. have a nice weekend! arvind. ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, March 15, 2019 7:44:32 PM To: Arvind SHARMA Cc: chimera List Subject: Re: [Chimera-users] drawing axes of rotational symmetry length: no width: not in the “measure rotation” command, but it’s essentially a stick bond between two fake atoms (markers), so you can use any of the same methods you could use to change stick bond thickness. For example, Ctrl-click the axis from “measure rotation" to select it and then open Selection Inspector (e.g. click green magnifying glass icon near lower right of window), inspect: bond, change radius. Then the markers on the ends will be bigger than the bond in between, but you could also select those markers (just like atoms, ctrl-click, Shift-ctrl-click) inspect: Atom, change radius to match the bond. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html> Or you could use the information in the Log to make your own 3D objects by defining them in a BILD-format file (simple text for cylinders, cones, etc.) and then opening that BILD file in Chimera. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html> I hope this helps, Elaine
On Mar 15, 2019, at 11:12 AM, Arvind SHARMA <arvind.sharma@pasteur.fr> wrote:
Hi Elaine,
thanks a lot. Its perfect, exactly what I needed! Just one more question, is there a way to control the length and width of the rotation axis rod?
best wishes, Arvind
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, March 15, 2019 5:48:36 PM To: Arvind SHARMA Cc: chimera List Subject: Re: [Chimera-users] drawing axes of rotational symmetry
Hi Arvind, Here is one approach:
(1) open the structure twice (as two models in Chimera, #0 and #1)
(2) superimpose domain A of one model onto domain B of the other model, using whatever method you prefer (“match” command specifying the exact atoms to use, or “matchmaker” command or GUI which uses CA atoms only and figures out the residue pairing for you, or even by hand, although that is usually harder)
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>
(3) use “measure rotation #0 #1” which will also display an axis (see options for axis color, slab display to show rotation and shift, etc.). Other things like shift and rotation angle are reported in the Log. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation>
(4) then you could hide or close one copy of the structure since it was only used to figure out this rotation
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 15, 2019, at 8:59 AM, Arvind SHARMA <arvind.sharma@pasteur.fr> wrote:
Hi, I would like to calculate the rotation axis between two domains of a protein (domains are highly similar in fold and sequence). Is there a way to calculate transformation matrix between two objects in chimera (two domains here) to obtain the direction of rotation axis and rotation angle values? Also is it possible to generate a translation vector along rotation axis in graphic screen? Would be great if there is a script available for that and someone can share.
Have a lovely weekend, arvind.
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Elaine Meng