question regarding relative rotation
Dear Chimera team, I would like to rotate a protein chain with respect to an axis that I define, but I cannot seem to find any way to do that. I have defined the axis, but the turn command will not allow me to use this as the center of rotation. I have also tried constrained motion, but this does not seem to have the parameters needed to do this. Is there a command or a menu that permits rotating a chain or structure around an axis you define yourself? Kr, Jannick
Dear Jannick, If you mean an axis object defined with Axes/Planes/Centroids or the "define" command, yes, you can rotate about that axis with the command "turn" or "roll" -- both ChimeraX and Chimera have this capability. It is the axis argument, not the center. See the help page for Chimera "turn": <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> Example commands: open 1zik define axis :.a turn a1 40 To set up a rotation around that axis with the mouse in Chimera, you'd need to look in the Reply Log when creating the axis (or use the Save button on Axes/Planes/Centroids to save to a text file) to get the axis information and then enter corresponding axis and origin coordinates into the Constrained Move tool. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/constrained/constrained.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2023, at 1:07 PM, Jannick Cornelius Snel-Prentø via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera team,
I would like to rotate a protein chain with respect to an axis that I define, but I cannot seem to find any way to do that. I have defined the axis, but the turn command will not allow me to use this as the center of rotation. I have also tried constrained motion, but this does not seem to have the parameters needed to do this. Is there a command or a menu that permits rotating a chain or structure around an axis you define yourself?
Kr, Jannick _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Thanks so much for the rapid response. I have defined the axis "a1" as seen in the attached png, but when I run the command: turn axis a1, angle 45, model 0 I get this error: turn axis argument must be "x", "y", or "z" or 3 numbers separated by commas, a defined axis (see "define" command), or a specifier for a bond or pair of atoms I have tried many things to fix this, but I can't seem to get Chimera to use the defined axis, although it is listed in the axis table. Chatgpt can't help. Any help with this? -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 19. maj 2023 22:56 To: Jannick Cornelius Snel-Prentø <jprentoe@sund.ku.dk> Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] question regarding relative rotation [You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Dear Jannick, If you mean an axis object defined with Axes/Planes/Centroids or the "define" command, yes, you can rotate about that axis with the command "turn" or "roll" -- both ChimeraX and Chimera have this capability. It is the axis argument, not the center. See the help page for Chimera "turn": <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> Example commands: open 1zik define axis :.a turn a1 40 To set up a rotation around that axis with the mouse in Chimera, you'd need to look in the Reply Log when creating the axis (or use the Save button on Axes/Planes/Centroids to save to a text file) to get the axis information and then enter corresponding axis and origin coordinates into the Constrained Move tool. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/constrained/constrained.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2023, at 1:07 PM, Jannick Cornelius Snel-Prentø via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera team,
I would like to rotate a protein chain with respect to an axis that I define, but I cannot seem to find any way to do that. I have defined the axis, but the turn command will not allow me to use this as the center of rotation. I have also tried constrained motion, but this does not seem to have the parameters needed to do this. Is there a command or a menu that permits rotating a chain or structure around an axis you define yourself?
Kr, Jannick _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www/. rbvi.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=05%7C01%7Cjpre ntoe%40sund.ku.dk%7Cf9b126f143ab43ae87b708db58ab8589%7Ca3927f91cda1469 6af898c9f1ceffa91%7C0%7C0%7C638201265929655575%7CUnknown%7CTWFpbGZsb3d 8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C 3000%7C%7C%7C&sdata=1Qc%2BAgvpYGc7ONy4HESNv285%2Fuqvdo1ogdMp5b9Dfn4%3D &reserved=0
Hi Jannick, The command does not contain the words "axis" or "angle" ... they are in italics in the usage, which means they would be replaced by the actual value. I already showed you this in the example in my previous reply:
Example commands: open 1zik define axis :.a turn a1 40
... which will turn around axis a1 with angle 40 degrees. Or, substituting your values: turn a1 45 model #0
See the help page for Chimera "turn": <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html>
Don't use chatgpt, it will just make up convincing-sounding wrong answer. Use the User Guide and its examples, and answers by real people like me or other users on this list. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2023, at 11:34 PM, Jannick Cornelius Snel-Prentø via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Thanks so much for the rapid response. I have defined the axis "a1" as seen in the attached png, but when I run the command:
turn axis a1, angle 45, model 0
I get this error:
turn axis argument must be "x", "y", or "z" or 3 numbers separated by commas, a defined axis (see "define" command), or a specifier for a bond or pair of atoms
I have tried many things to fix this, but I can't seem to get Chimera to use the defined axis, although it is listed in the axis table. Chatgpt can't help.
Any help with this?
-----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 19. maj 2023 22:56 To: Jannick Cornelius Snel-Prentø <jprentoe@sund.ku.dk> Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] question regarding relative rotation
[You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]
Dear Jannick, If you mean an axis object defined with Axes/Planes/Centroids or the "define" command, yes, you can rotate about that axis with the command "turn" or "roll" -- both ChimeraX and Chimera have this capability. It is the axis argument, not the center. See the help page for Chimera "turn": <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html>
Example commands: open 1zik define axis :.a turn a1 40
To set up a rotation around that axis with the mouse in Chimera, you'd need to look in the Reply Log when creating the axis (or use the Save button on Axes/Planes/Centroids to save to a text file) to get the axis information and then enter corresponding axis and origin coordinates into the Constrained Move tool. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/constrained/constrained.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2023, at 1:07 PM, Jannick Cornelius Snel-Prentø via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera team,
I would like to rotate a protein chain with respect to an axis that I define, but I cannot seem to find any way to do that. I have defined the axis, but the turn command will not allow me to use this as the center of rotation. I have also tried constrained motion, but this does not seem to have the parameters needed to do this. Is there a command or a menu that permits rotating a chain or structure around an axis you define yourself?
Kr, Jannick
Thank so much Elaine, this works and was super helpful! Br, Jannick -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 21. maj 2023 18:25 To: Jannick Cornelius Snel-Prentø <jprentoe@sund.ku.dk> Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] question regarding relative rotation [You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Hi Jannick, The command does not contain the words "axis" or "angle" ... they are in italics in the usage, which means they would be replaced by the actual value. I already showed you this in the example in my previous reply:
Example commands: open 1zik define axis :.a turn a1 40
... which will turn around axis a1 with angle 40 degrees. Or, substituting your values: turn a1 45 model #0
See the help page for Chimera "turn": <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww .rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fturn.html&data= 05%7C01%7Cjprentoe%40sund.ku.dk%7Ceecc2e4e7c474d605ff008db5a17fdad%7Ca 3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C638202831338263478%7CUnknown %7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJ XVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=WPY%2FCYFlAy8jblRFBL2ynCBq50SnJGWpr5 BXWRigIzk%3D&reserved=0>
Don't use chatgpt, it will just make up convincing-sounding wrong answer. Use the User Guide and its examples, and answers by real people like me or other users on this list. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2023, at 11:34 PM, Jannick Cornelius Snel-Prentø via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Thanks so much for the rapid response. I have defined the axis "a1" as seen in the attached png, but when I run the command:
turn axis a1, angle 45, model 0
I get this error:
turn axis argument must be "x", "y", or "z" or 3 numbers separated by commas, a defined axis (see "define" command), or a specifier for a bond or pair of atoms
I have tried many things to fix this, but I can't seem to get Chimera to use the defined axis, although it is listed in the axis table. Chatgpt can't help.
Any help with this?
-----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 19. maj 2023 22:56 To: Jannick Cornelius Snel-Prentø <jprentoe@sund.ku.dk> Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] question regarding relative rotation
[You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]
Dear Jannick, If you mean an axis object defined with Axes/Planes/Centroids or the "define" command, yes, you can rotate about that axis with the command "turn" or "roll" -- both ChimeraX and Chimera have this capability. It is the axis argument, not the center. See the help page for Chimera "turn": <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww .rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fturn.html&data= 05%7C01%7Cjprentoe%40sund.ku.dk%7Ceecc2e4e7c474d605ff008db5a17fdad%7Ca 3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C638202831338263478%7CUnknown %7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJ XVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=WPY%2FCYFlAy8jblRFBL2ynCBq50SnJGWpr5 BXWRigIzk%3D&reserved=0>
Example commands: open 1zik define axis :.a turn a1 40
To set up a rotation around that axis with the mouse in Chimera, you'd need to look in the Reply Log when creating the axis (or use the Save button on Axes/Planes/Centroids to save to a text file) to get the axis information and then enter corresponding axis and origin coordinates into the Constrained Move tool. <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww .rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fconstrained%2F constrained.html&data=05%7C01%7Cjprentoe%40sund.ku.dk%7Ceecc2e4e7c474d 605ff008db5a17fdad%7Ca3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C638202 831338263478%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luM zIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=tpWVZs65l3v0j0 bbgm%2F8%2FR0QtvGLvihpEIPKcFwbeqg%3D&reserved=0>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2023, at 1:07 PM, Jannick Cornelius Snel-Prentø via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera team,
I would like to rotate a protein chain with respect to an axis that I define, but I cannot seem to find any way to do that. I have defined the axis, but the turn command will not allow me to use this as the center of rotation. I have also tried constrained motion, but this does not seem to have the parameters needed to do this. Is there a command or a menu that permits rotating a chain or structure around an axis you define yourself?
Kr, Jannick
participants (2)
-
Elaine Meng -
Jannick Cornelius Snel-Prentø