Hi, I are trying to use Chimera to produce duplicates of one fibrinogen, rotate and move them, and concatenate together in a certain way. The fibrinogen looks like this (http://dl.dropbox.com/u/3757507/chimera1.png). I want to duplicate the model, and connect them in a chain (http://dl.dropbox.com/u/3757507/chimera2.png). The second image shows only two instances, but there will be more. Currently I do it by hand, including rotating and aligning them in correct z positions. But it take a lot of time to do it because the duplicates generated by using Tools/Higher-order structure/Unit Cell are not in the same plane. I have to look back and forth in different directions to make sure them are aligned. So I are wondering is there any way to automate this process, such as apply the previous transformation to a new duplicate? Thanks, Joe
Hi Joe, Hmm, well, you could measure the transformation between your first and second copies with "measure rotation." Then, if that corresponds to some symmetry group or product of groups, you could generate multiple additional copies with a single "sym" command using the "group" option. <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html> However, I'm not sure how easy or difficult it would be to figure out the necessary sym command from the information given in the Reply Log from the measure command, i.e. whether it is a simple helical relationship or something more complicated. Maybe a python script to repeatedly apply the transformation to additional copies would be more effective (beyond my skill set, sorry). I'm not the most knowledgable here on this particular topic; perhaps the others will have clearer ideas of how to attack the problem, or a script. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 11, 2011, at 1:04 PM, Joe Ping-Lin Hsiao wrote:
Hi, I are trying to use Chimera to produce duplicates of one fibrinogen, rotate and move them, and concatenate together in a certain way. The fibrinogen looks like this (http://dl.dropbox.com/u/3757507/chimera1.png). I want to duplicate the model, and connect them in a chain (http://dl.dropbox.com/u/3757507/chimera2.png). The second image shows only two instances, but there will be more.
Currently I do it by hand, including rotating and aligning them in correct z positions. But it take a lot of time to do it because the duplicates generated by using Tools/Higher-order structure/Unit Cell are not in the same plane. I have to look back and forth in different directions to make sure them are aligned. So I are wondering is there any way to automate this process, such as apply the previous transformation to a new duplicate?
Thanks, Joe
Hi Joe, Elaine's suggestion is the way to go. If you have two copies of your molecule #0 and #1 and you want to add additional subunits use the "measure rotation" and the sym commands to do it. Here's an example. Notice I take the axis, axis point, rotation angle, and shift along axis from the measure rotation and use those in the "sym" command to create 4 additional copies using helical symmetry. A single rotation and translation always specifies a helical symmetry (rotation about an axis and shift along that axis). In the case where the shift along the axis is 0 you get cyclic symmetry. You'll probably find the "sym" command documentation useful http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html Tom measure rotation #0 #1 Reply log: Position of 1E6J (#1) relative to 1E6J (#0) coordinates: Matrix rotation and translation 0.96949029 -0.23745478 -0.06085881 98.69560733 0.03663564 0.38584119 -0.92183752 7.88875940 0.24237657 0.89148292 0.38276860 7.78837497 Axis 0.97552284 -0.16313335 0.14745407 Axis point 0.00000000 17.01960113 14.23231084 Rotation angle (degrees) 68.34295730 Shift along axis 96.14132684 sym #1 group h,96.14,68.34,5 axis 0.9755,-0.1631,0.14745 center 0,17.02,14.23 coord #0
Hi Joe, Hmm, well, you could measure the transformation between your first and second copies with "measure rotation." Then, if that corresponds to some symmetry group or product of groups, you could generate multiple additional copies with a single "sym" command using the "group" option.
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>
However, I'm not sure how easy or difficult it would be to figure out the necessary sym command from the information given in the Reply Log from the measure command, i.e. whether it is a simple helical relationship or something more complicated. Maybe a python script to repeatedly apply the transformation to additional copies would be more effective (beyond my skill set, sorry).
I'm not the most knowledgable here on this particular topic; perhaps the others will have clearer ideas of how to attack the problem, or a script. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2011, at 1:04 PM, Joe Ping-Lin Hsiao wrote:
Hi, I are trying to use Chimera to produce duplicates of one fibrinogen, rotate and move them, and concatenate together in a certain way. The fibrinogen looks like this (http://dl.dropbox.com/u/3757507/chimera1.png). I want to duplicate the model, and connect them in a chain (http://dl.dropbox.com/u/3757507/chimera2.png). The second image shows only two instances, but there will be more.
Currently I do it by hand, including rotating and aligning them in correct z positions. But it take a lot of time to do it because the duplicates generated by using Tools/Higher-order structure/Unit Cell are not in the same plane. I have to look back and forth in different directions to make sure them are aligned. So I are wondering is there any way to automate this process, such as apply the previous transformation to a new duplicate?
Thanks, Joe
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks, Elaine and Tom, Tom, I tried what you suggested but only generating one extra copy of model #1. But sym command created a weird-looking model at the same place where the original #1 is (http://dl.dropbox.com/u/3757507/chinema3.png). Below is the output of my "measure rotation #0 #1": Position of single_3ghg_monomer.pdb #2 (#1) relative to single_3ghg_monomer.pdb (#0) coordinates: Matrix rotation and translation 0.79947388 0.29593455 -0.52274683 66.20071818 -0.40522870 -0.37669835 -0.83299943 -113.45813726 -0.44343118 0.87779331 -0.18123932 -31.01344468 Axis 0.92445135 -0.04285935 -0.37888360 Axis point 0.00000000 -54.63874726 -41.89926982 Rotation angle (degrees) 112.28611242 Shift along axis 77.81257053 And the sym command I used is: sym #1 group h,77.81,112.286,2 axis 0.92445,-0.04286,-0.37888 center 0,-54.6387,-41.89927 coord #0 Thanks, Joe On Tue, Oct 11, 2011 at 6:42 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Joe,
Elaine's suggestion is the way to go. If you have two copies of your molecule #0 and #1 and you want to add additional subunits use the "measure rotation" and the sym commands to do it. Here's an example. Notice I take the axis, axis point, rotation angle, and shift along axis from the measure rotation and use those in the "sym" command to create 4 additional copies using helical symmetry. A single rotation and translation always specifies a helical symmetry (rotation about an axis and shift along that axis). In the case where the shift along the axis is 0 you get cyclic symmetry.
You'll probably find the "sym" command documentation useful
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html
Tom
measure rotation #0 #1
Reply log: Position of 1E6J (#1) relative to 1E6J (#0) coordinates: Matrix rotation and translation 0.96949029 -0.23745478 -0.06085881 98.69560733 0.03663564 0.38584119 -0.92183752 7.88875940 0.24237657 0.89148292 0.38276860 7.78837497 Axis 0.97552284 -0.16313335 0.14745407 Axis point 0.00000000 17.01960113 14.23231084 Rotation angle (degrees) 68.34295730 Shift along axis 96.14132684
sym #1 group h,96.14,68.34,5 axis 0.9755,-0.1631,0.14745 center 0,17.02,14.23 coord #0
Hi Joe, Hmm, well, you could measure the transformation between your first and second copies with "measure rotation." Then, if that corresponds to some symmetry group or product of groups, you could generate multiple additional copies with a single "sym" command using the "group" option.
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>
However, I'm not sure how easy or difficult it would be to figure out the necessary sym command from the information given in the Reply Log from the measure command, i.e. whether it is a simple helical relationship or something more complicated. Maybe a python script to repeatedly apply the transformation to additional copies would be more effective (beyond my skill set, sorry).
I'm not the most knowledgable here on this particular topic; perhaps the others will have clearer ideas of how to attack the problem, or a script. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2011, at 1:04 PM, Joe Ping-Lin Hsiao wrote:
Hi, I are trying to use Chimera to produce duplicates of one fibrinogen, rotate and move them, and concatenate together in a certain way. The fibrinogen looks like this (http://dl.dropbox.com/u/3757507/chimera1.png). I want to duplicate the model, and connect them in a chain (http://dl.dropbox.com/u/3757507/chimera2.png). The second image shows only two instances, but there will be more.
Currently I do it by hand, including rotating and aligning them in correct z positions. But it take a lot of time to do it because the duplicates generated by using Tools/Higher-order structure/Unit Cell are not in the same plane. I have to look back and forth in different directions to make sure them are aligned. So I are wondering is there any way to automate this process, such as apply the previous transformation to a new duplicate?
Thanks, Joe
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Joe, I suspect the sym command made the molecule copy in the wrong place because the two original copies of 3ghg (#0 and #1) do not have the same atom coordinates. This causes the measure rotation command to give the wrong rotation parameters. This would happen if your two original copies came from the Unit Cell dialog. That dialog creates copies of the molecule with different atom coordinates. Instead you want to start with two copies of 3ghg with identical atom coordinates -- for example just open it twice. open 3ghg open 3ghg 3ghg contains two copies of the coiled coil so delete one copy del :.G-L,.Q-T Now move model #1 relative to model #0 as you like. Then use measure rotation and the sym command. I did this and it worked fine as shown in the attached image. The reason this is different from using two copies of the molecule made by unit cell is rather technical. The unit cell dialog makes copies of the molecules where the atoms have different x,y,z coordinates in the two copies. The procedure I just described uses two molecule copies with the same atom coordinates but the models have different coordinate systems. Moving one molecule relative to the other just changes the coordinate system of the moved molecule, not the actual atom x,y,z coordinate values. The second problem you observed is that the molecule made by the sym command appears wrong -- as if it has all kinds of long bonds. This could be a bug in the code that makes the molecule copy or a bug in your graphics driver. I don't see that with Mac Chimera. If you can make it happen again, then save a session and use menu Help / Report a Bug..., say the molecule drawing is wrong, and attach the session file. Tom
Thanks, Elaine and Tom,
Tom, I tried what you suggested but only generating one extra copy of model #1. But sym command created a weird-looking model at the same place where the original #1 is (http://dl.dropbox.com/u/3757507/chinema3.png).
Below is the output of my "measure rotation #0 #1":
Position of single_3ghg_monomer.pdb #2 (#1) relative to single_3ghg_monomer.pdb (#0) coordinates: Matrix rotation and translation 0.79947388 0.29593455 -0.52274683 66.20071818 -0.40522870 -0.37669835 -0.83299943 -113.45813726 -0.44343118 0.87779331 -0.18123932 -31.01344468 Axis 0.92445135 -0.04285935 -0.37888360 Axis point 0.00000000 -54.63874726 -41.89926982 Rotation angle (degrees) 112.28611242 Shift along axis 77.81257053
And the sym command I used is:
sym #1 group h,77.81,112.286,2 axis 0.92445,-0.04286,-0.37888 center 0,-54.6387,-41.89927 coord #0
Thanks, Joe
On Tue, Oct 11, 2011 at 6:42 PM, Tom Goddard<goddard@sonic.net> wrote:
Hi Joe,
Elaine's suggestion is the way to go. If you have two copies of your molecule #0 and #1 and you want to add additional subunits use the "measure rotation" and the sym commands to do it. Here's an example. Notice I take the axis, axis point, rotation angle, and shift along axis from the measure rotation and use those in the "sym" command to create 4 additional copies using helical symmetry. A single rotation and translation always specifies a helical symmetry (rotation about an axis and shift along that axis). In the case where the shift along the axis is 0 you get cyclic symmetry.
You'll probably find the "sym" command documentation useful
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html
Tom
measure rotation #0 #1
Reply log: Position of 1E6J (#1) relative to 1E6J (#0) coordinates: Matrix rotation and translation 0.96949029 -0.23745478 -0.06085881 98.69560733 0.03663564 0.38584119 -0.92183752 7.88875940 0.24237657 0.89148292 0.38276860 7.78837497 Axis 0.97552284 -0.16313335 0.14745407 Axis point 0.00000000 17.01960113 14.23231084 Rotation angle (degrees) 68.34295730 Shift along axis 96.14132684
sym #1 group h,96.14,68.34,5 axis 0.9755,-0.1631,0.14745 center 0,17.02,14.23 coord #0
Hi Joe, Hmm, well, you could measure the transformation between your first and second copies with "measure rotation." Then, if that corresponds to some symmetry group or product of groups, you could generate multiple additional copies with a single "sym" command using the "group" option.
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>
However, I'm not sure how easy or difficult it would be to figure out the necessary sym command from the information given in the Reply Log from the measure command, i.e. whether it is a simple helical relationship or something more complicated. Maybe a python script to repeatedly apply the transformation to additional copies would be more effective (beyond my skill set, sorry).
I'm not the most knowledgable here on this particular topic; perhaps the others will have clearer ideas of how to attack the problem, or a script. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2011, at 1:04 PM, Joe Ping-Lin Hsiao wrote:
Hi, I are trying to use Chimera to produce duplicates of one fibrinogen, rotate and move them, and concatenate together in a certain way. The fibrinogen looks like this (http://dl.dropbox.com/u/3757507/chimera1.png). I want to duplicate the model, and connect them in a chain (http://dl.dropbox.com/u/3757507/chimera2.png). The second image shows only two instances, but there will be more.
Currently I do it by hand, including rotating and aligning them in correct z positions. But it take a lot of time to do it because the duplicates generated by using Tools/Higher-order structure/Unit Cell are not in the same plane. I have to look back and forth in different directions to make sure them are aligned. So I are wondering is there any way to automate this process, such as apply the previous transformation to a new duplicate?
Thanks, Joe
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
It works! Thanks a lot, Tom! I also tested it on a Mac. The trick is to download a "Daily Build" Chimera. In a "Current Production Release", I would get warning message "no symmetric molecules are selected" if I try to send a "sym" command. I'll try it on Windows later. Thanks again! Joe On Wed, Oct 12, 2011 at 6:13 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Joe,
I suspect the sym command made the molecule copy in the wrong place because the two original copies of 3ghg (#0 and #1) do not have the same atom coordinates. This causes the measure rotation command to give the wrong rotation parameters. This would happen if your two original copies came from the Unit Cell dialog. That dialog creates copies of the molecule with different atom coordinates. Instead you want to start with two copies of 3ghg with identical atom coordinates -- for example just open it twice.
open 3ghg open 3ghg
3ghg contains two copies of the coiled coil so delete one copy
del :.G-L,.Q-T
Now move model #1 relative to model #0 as you like. Then use measure rotation and the sym command. I did this and it worked fine as shown in the attached image. The reason this is different from using two copies of the molecule made by unit cell is rather technical. The unit cell dialog makes copies of the molecules where the atoms have different x,y,z coordinates in the two copies. The procedure I just described uses two molecule copies with the same atom coordinates but the models have different coordinate systems. Moving one molecule relative to the other just changes the coordinate system of the moved molecule, not the actual atom x,y,z coordinate values.
The second problem you observed is that the molecule made by the sym command appears wrong -- as if it has all kinds of long bonds. This could be a bug in the code that makes the molecule copy or a bug in your graphics driver. I don't see that with Mac Chimera. If you can make it happen again, then save a session and use menu Help / Report a Bug..., say the molecule drawing is wrong, and attach the session file.
Tom
Thanks, Elaine and Tom,
Tom, I tried what you suggested but only generating one extra copy of model #1. But sym command created a weird-looking model at the same place where the original #1 is (http://dl.dropbox.com/u/3757507/chinema3.png).
Below is the output of my "measure rotation #0 #1":
Position of single_3ghg_monomer.pdb #2 (#1) relative to single_3ghg_monomer.pdb (#0) coordinates: Matrix rotation and translation 0.79947388 0.29593455 -0.52274683 66.20071818 -0.40522870 -0.37669835 -0.83299943 -113.45813726 -0.44343118 0.87779331 -0.18123932 -31.01344468 Axis 0.92445135 -0.04285935 -0.37888360 Axis point 0.00000000 -54.63874726 -41.89926982 Rotation angle (degrees) 112.28611242 Shift along axis 77.81257053
And the sym command I used is:
sym #1 group h,77.81,112.286,2 axis 0.92445,-0.04286,-0.37888 center 0,-54.6387,-41.89927 coord #0
Thanks, Joe
On Tue, Oct 11, 2011 at 6:42 PM, Tom Goddard<goddard@sonic.net> wrote:
Hi Joe,
Elaine's suggestion is the way to go. If you have two copies of your molecule #0 and #1 and you want to add additional subunits use the "measure rotation" and the sym commands to do it. Here's an example. Notice I take the axis, axis point, rotation angle, and shift along axis from the measure rotation and use those in the "sym" command to create 4 additional copies using helical symmetry. A single rotation and translation always specifies a helical symmetry (rotation about an axis and shift along that axis). In the case where the shift along the axis is 0 you get cyclic symmetry.
You'll probably find the "sym" command documentation useful
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html
Tom
measure rotation #0 #1
Reply log: Position of 1E6J (#1) relative to 1E6J (#0) coordinates: Matrix rotation and translation 0.96949029 -0.23745478 -0.06085881 98.69560733 0.03663564 0.38584119 -0.92183752 7.88875940 0.24237657 0.89148292 0.38276860 7.78837497 Axis 0.97552284 -0.16313335 0.14745407 Axis point 0.00000000 17.01960113 14.23231084 Rotation angle (degrees) 68.34295730 Shift along axis 96.14132684
sym #1 group h,96.14,68.34,5 axis 0.9755,-0.1631,0.14745 center 0,17.02,14.23 coord #0
Hi Joe, Hmm, well, you could measure the transformation between your first and second copies with "measure rotation." Then, if that corresponds to some symmetry group or product of groups, you could generate multiple additional copies with a single "sym" command using the "group" option.
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>
However, I'm not sure how easy or difficult it would be to figure out the necessary sym command from the information given in the Reply Log from the measure command, i.e. whether it is a simple helical relationship or something more complicated. Maybe a python script to repeatedly apply the transformation to additional copies would be more effective (beyond my skill set, sorry).
I'm not the most knowledgable here on this particular topic; perhaps the others will have clearer ideas of how to attack the problem, or a script. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2011, at 1:04 PM, Joe Ping-Lin Hsiao wrote:
Hi, I are trying to use Chimera to produce duplicates of one fibrinogen, rotate and move them, and concatenate together in a certain way. The fibrinogen looks like this (http://dl.dropbox.com/u/3757507/chimera1.png). I want to duplicate the model, and connect them in a chain (http://dl.dropbox.com/u/3757507/chimera2.png). The second image shows only two instances, but there will be more.
Currently I do it by hand, including rotating and aligning them in correct z positions. But it take a lot of time to do it because the duplicates generated by using Tools/Higher-order structure/Unit Cell are not in the same plane. I have to look back and forth in different directions to make sure them are aligned. So I are wondering is there any way to automate this process, such as apply the previous transformation to a new duplicate?
Thanks, Joe
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
One more idea if the crystal does contain the desired superstructure (which it might not) is to play around with the Options in the Unit Cell dialog. Namely, whether the molecules are "packed" or not, and the number of cells in each direction to be built. Elaine On Oct 11, 2011, at 1:04 PM, Joe Ping-Lin Hsiao wrote:
Hi,
I are trying to use Chimera to produce duplicates of one fibrinogen, rotate and move them, and concatenate together in a certain way. The fibrinogen looks like this (http://dl.dropbox.com/u/3757507/chimera1.png). I want to duplicate the model, and connect them in a chain (http://dl.dropbox.com/u/3757507/chimera2.png). The second image shows only two instances, but there will be more.
Currently I do it by hand, including rotating and aligning them in correct z positions. But it take a lot of time to do it because the duplicates generated by using Tools/Higher-order structure/Unit Cell are not in the same plane. I have to look back and forth in different directions to make sure them are aligned. So I are wondering is there any way to automate this process, such as apply the previous transformation to a new duplicate?
Thanks, Joe
participants (3)
-
Elaine Meng -
Joe Ping-Lin Hsiao -
Tom Goddard