Hi, I would like to highlight a hole in a protein -the exit tunnel of a ribosome, to be more specific. I tried the command shape tube in order to draw three tubes passing through three residues, but the result doesn't suit at best my need and expectations. Is possible to draw a circle, passing through three points -or residues-? Do you have any suggestions? Thank you for your attention. Have a great week end. Greetings, Andrea
Hi Andrea, You can add a "2D label" that is a circle symbol, and adjust its size (fontsize) and color however you like, and position it manually by dragging. It's not a part of the 3D scene but a label pasted on top. Maybe this will meet your needs. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/2dlabels.html> You would first add the label with the 2Dlabel command, and then manually drag to reposition and use 2dlabel command again to change size as needed. The text of the label is given with the "text" option, and symbols can be specified as unicode, or pasted in after copying, e.g. from this page: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/symbols.html> Example commands, and see attached image: open 1gcn show :lys 2dlab text ◯ size 40 color yellow bold true ... where the circle was copied from the symbols page linked above and pasted into the command line. Next, I decide that is too small. I can see model number of this label is #2.1 in Models panel, so to enlarge it: 2dlab #2.1 size 80 ... then to drag by hand, assign a mouse mode using the Right Mouse tab of the toolbar across the top of the Chimerax window. The icon with text "ATP" and arrow under it is the move-label mouse mode. Click that to assign right mouse to dragging the label (it will execute command: ui mousemode right "move label" ). Then you can use the right mouse button (= trackpad + Alt on Windows, trackpad + command on Mac) to drag the label, in this case the circle. <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.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 Aug 15, 2020, at 8:43 AM, Andrea Dallapè <andrea.dallape@unitn.it> wrote:
Hi,
I would like to highlight a hole in a protein -the exit tunnel of a ribosome, to be more specific. I tried the command shape tube in order to draw three tubes passing through three residues, but the result doesn't suit at best my need and expectations. Is possible to draw a circle, passing through three points -or residues-? Do you have any suggestions? Thank you for your attention. Have a great week end. Greetings,
Andrea _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Elaine, thank you for your prompt and kind reply. Unfortunately, it doesn't help me. I don't want to merely highlight the exit tunnel for an image, but, given some residues around them, I want to find and highlight it. I have multiple ribosomes in a map and I want to assess and compare the orientation of the exit tunnel of every ribosome, in order to study if any preferential orientation is found. Labeling it doesn't suit my needs. Do you have any other suggestions? Thank you for your attention. Have a nice day, Andrea Il giorno sab 15 ago 2020 alle ore 18:07 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Hi Andrea, You can add a "2D label" that is a circle symbol, and adjust its size (fontsize) and color however you like, and position it manually by dragging. It's not a part of the 3D scene but a label pasted on top. Maybe this will meet your needs.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/2dlabels.html>
You would first add the label with the 2Dlabel command, and then manually drag to reposition and use 2dlabel command again to change size as needed. The text of the label is given with the "text" option, and symbols can be specified as unicode, or pasted in after copying, e.g. from this page:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/symbols.html>
Example commands, and see attached image:
open 1gcn show :lys 2dlab text ◯ size 40 color yellow bold true
... where the circle was copied from the symbols page linked above and pasted into the command line. Next, I decide that is too small. I can see model number of this label is #2.1 in Models panel, so to enlarge it:
2dlab #2.1 size 80
... then to drag by hand, assign a mouse mode using the Right Mouse tab of the toolbar across the top of the Chimerax window. The icon with text "ATP" and arrow under it is the move-label mouse mode. Click that to assign right mouse to dragging the label (it will execute command: ui mousemode right "move label" ). Then you can use the right mouse button (= trackpad + Alt on Windows, trackpad + command on Mac) to drag the label, in this case the circle.
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.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 Aug 15, 2020, at 8:43 AM, Andrea Dallapè <andrea.dallape@unitn.it> wrote:
Hi,
I would like to highlight a hole in a protein -the exit tunnel of a ribosome, to be more specific. I tried the command shape tube in order to draw three tubes passing through three residues, but the result doesn't suit at best my need and expectations. Is possible to draw a circle, passing through three points -or residues-? Do you have any suggestions? Thank you for your attention. Have a great week end. Greetings,
Andrea _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Andrea, In that case you might want to take a look at "define plane" for each set of residues. It will make a (planar) disc fit to the specified atoms, and you can can choose the color, including transparency, of the disc. example: open 1g74 define plane :17,20,74@ca color 100,0,0,50 define plane :4,11,130@ca color 0,20,80,50 <http://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#plane> You can also specify these planes (discs) in distance measurements with the "distance" command, but not yet in angle measurements. The normals to the planes are reported in the Log so you could calculate angles yourself manually. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html> Our older program Chimera has defining planes (Axes/Planes/Centroids tool or "define" command) as well as measuring angles and distances among them, but is much slower on large structures like ribosomes. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru...> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 17, 2020, at 2:14 AM, Andrea Dallapè <andrea.dallape@unitn.it> wrote:
Hi Elaine,
thank you for your prompt and kind reply. Unfortunately, it doesn't help me. I don't want to merely highlight the exit tunnel for an image, but, given some residues around them, I want to find and highlight it. I have multiple ribosomes in a map and I want to assess and compare the orientation of the exit tunnel of every ribosome, in order to study if any preferential orientation is found. Labeling it doesn't suit my needs. Do you have any other suggestions? Thank you for your attention. Have a nice day,
Andrea
Il giorno sab 15 ago 2020 alle ore 18:07 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: Hi Andrea, You can add a "2D label" that is a circle symbol, and adjust its size (fontsize) and color however you like, and position it manually by dragging. It's not a part of the 3D scene but a label pasted on top. Maybe this will meet your needs.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/2dlabels.html>
You would first add the label with the 2Dlabel command, and then manually drag to reposition and use 2dlabel command again to change size as needed. The text of the label is given with the "text" option, and symbols can be specified as unicode, or pasted in after copying, e.g. from this page:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/symbols.html>
Example commands, and see attached image:
open 1gcn show :lys 2dlab text ◯ size 40 color yellow bold true
... where the circle was copied from the symbols page linked above and pasted into the command line. Next, I decide that is too small. I can see model number of this label is #2.1 in Models panel, so to enlarge it:
2dlab #2.1 size 80
... then to drag by hand, assign a mouse mode using the Right Mouse tab of the toolbar across the top of the Chimerax window. The icon with text "ATP" and arrow under it is the move-label mouse mode. Click that to assign right mouse to dragging the label (it will execute command: ui mousemode right "move label" ). Then you can use the right mouse button (= trackpad + Alt on Windows, trackpad + command on Mac) to drag the label, in this case the circle.
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<2dcircle.png>
On Aug 15, 2020, at 8:43 AM, Andrea Dallapè <andrea.dallape@unitn.it> wrote:
Hi,
I would like to highlight a hole in a protein -the exit tunnel of a ribosome, to be more specific. I tried the command shape tube in order to draw three tubes passing through three residues, but the result doesn't suit at best my need and expectations. Is possible to draw a circle, passing through three points -or residues-? Do you have any suggestions? Thank you for your attention. Have a great week end. Greetings,
Andrea
Hi Elaine, thank you, this could help me! One problem, define plane command give me an error of unknown command. I even tried to copy and paste the code you wrote but it reiterate again such error. What I'm doing wrong? Thank you again for your patience and attention, Andrea Il giorno lun 17 ago 2020 alle ore 17:31 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Hi Andrea, In that case you might want to take a look at "define plane" for each set of residues. It will make a (planar) disc fit to the specified atoms, and you can can choose the color, including transparency, of the disc.
example: open 1g74 define plane :17,20,74@ca color 100,0,0,50 define plane :4,11,130@ca color 0,20,80,50
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#plane>
You can also specify these planes (discs) in distance measurements with the "distance" command, but not yet in angle measurements. The normals to the planes are reported in the Log so you could calculate angles yourself manually.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html>
Our older program Chimera has defining planes (Axes/Planes/Centroids tool or "define" command) as well as measuring angles and distances among them, but is much slower on large structures like ribosomes. < http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru...
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 17, 2020, at 2:14 AM, Andrea Dallapè <andrea.dallape@unitn.it> wrote:
Hi Elaine,
thank you for your prompt and kind reply. Unfortunately, it doesn't help me. I don't want to merely highlight the exit tunnel for an image, but, given some residues around them, I want to find and highlight it. I have multiple ribosomes in a map and I want to assess and compare the orientation of the exit tunnel of every ribosome, in order to study if any preferential orientation is found. Labeling it doesn't suit my needs. Do you have any other suggestions? Thank you for your attention. Have a nice day,
Andrea
Il giorno sab 15 ago 2020 alle ore 18:07 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: Hi Andrea, You can add a "2D label" that is a circle symbol, and adjust its size (fontsize) and color however you like, and position it manually by dragging. It's not a part of the 3D scene but a label pasted on top. Maybe this will meet your needs.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/2dlabels.html>
You would first add the label with the 2Dlabel command, and then manually drag to reposition and use 2dlabel command again to change size as needed. The text of the label is given with the "text" option, and symbols can be specified as unicode, or pasted in after copying, e.g. from this page:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/symbols.html>
Example commands, and see attached image:
open 1gcn show :lys 2dlab text ◯ size 40 color yellow bold true
... where the circle was copied from the symbols page linked above and pasted into the command line. Next, I decide that is too small. I can see model number of this label is #2.1 in Models panel, so to enlarge it:
2dlab #2.1 size 80
... then to drag by hand, assign a mouse mode using the Right Mouse tab of the toolbar across the top of the Chimerax window. The icon with text "ATP" and arrow under it is the move-label mouse mode. Click that to assign right mouse to dragging the label (it will execute command: ui mousemode right "move label" ). Then you can use the right mouse button (= trackpad + Alt on Windows, trackpad + command on Mac) to drag the label, in this case the circle.
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<2dcircle.png>
On Aug 15, 2020, at 8:43 AM, Andrea Dallapè <andrea.dallape@unitn.it> wrote:
Hi,
I would like to highlight a hole in a protein -the exit tunnel of a ribosome, to be more specific. I tried the command shape tube in order to draw three tubes passing through three residues, but the result doesn't suit at best my need and expectations. Is possible to draw a circle, passing through three points -or residues-? Do you have any suggestions? Thank you for your attention. Have a great week end. Greetings,
Andrea
Hi Andrea, Command "define plane" is in the current daily build but not release 1.0 -- sorry I forgot to mention that. This feature is newer than release 1.0. The daily builds are available on the download page: <http://www.rbvi.ucsf.edu/chimerax/download.html#daily> Change log with approximate dates of new features: <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 18, 2020, at 1:29 AM, Andrea Dallapè <andrea.dallape@unitn.it> wrote:
Hi Elaine,
thank you, this could help me! One problem, define plane command give me an error of unknown command. I even tried to copy and paste the code you wrote but it reiterate again such error. What I'm doing wrong? Thank you again for your patience and attention,
Andrea
Il giorno lun 17 ago 2020 alle ore 17:31 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: Hi Andrea, In that case you might want to take a look at "define plane" for each set of residues. It will make a (planar) disc fit to the specified atoms, and you can can choose the color, including transparency, of the disc.
example: open 1g74 define plane :17,20,74@ca color 100,0,0,50 define plane :4,11,130@ca color 0,20,80,50
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#plane>
You can also specify these planes (discs) in distance measurements with the "distance" command, but not yet in angle measurements. The normals to the planes are reported in the Log so you could calculate angles yourself manually.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html>
Our older program Chimera has defining planes (Axes/Planes/Centroids tool or "define" command) as well as measuring angles and distances among them, but is much slower on large structures like ribosomes. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru...>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 17, 2020, at 2:14 AM, Andrea Dallapè <andrea.dallape@unitn.it> wrote:
Hi Elaine,
thank you for your prompt and kind reply. Unfortunately, it doesn't help me. I don't want to merely highlight the exit tunnel for an image, but, given some residues around them, I want to find and highlight it. I have multiple ribosomes in a map and I want to assess and compare the orientation of the exit tunnel of every ribosome, in order to study if any preferential orientation is found. Labeling it doesn't suit my needs. Do you have any other suggestions? Thank you for your attention. Have a nice day,
Andrea
Il giorno sab 15 ago 2020 alle ore 18:07 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: Hi Andrea, You can add a "2D label" that is a circle symbol, and adjust its size (fontsize) and color however you like, and position it manually by dragging. It's not a part of the 3D scene but a label pasted on top. Maybe this will meet your needs.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/2dlabels.html>
You would first add the label with the 2Dlabel command, and then manually drag to reposition and use 2dlabel command again to change size as needed. The text of the label is given with the "text" option, and symbols can be specified as unicode, or pasted in after copying, e.g. from this page:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/symbols.html>
Example commands, and see attached image:
open 1gcn show :lys 2dlab text ◯ size 40 color yellow bold true
... where the circle was copied from the symbols page linked above and pasted into the command line. Next, I decide that is too small. I can see model number of this label is #2.1 in Models panel, so to enlarge it:
2dlab #2.1 size 80
... then to drag by hand, assign a mouse mode using the Right Mouse tab of the toolbar across the top of the Chimerax window. The icon with text "ATP" and arrow under it is the move-label mouse mode. Click that to assign right mouse to dragging the label (it will execute command: ui mousemode right "move label" ). Then you can use the right mouse button (= trackpad + Alt on Windows, trackpad + command on Mac) to drag the label, in this case the circle.
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<2dcircle.png>
On Aug 15, 2020, at 8:43 AM, Andrea Dallapè <andrea.dallape@unitn.it> wrote:
Hi,
I would like to highlight a hole in a protein -the exit tunnel of a ribosome, to be more specific. I tried the command shape tube in order to draw three tubes passing through three residues, but the result doesn't suit at best my need and expectations. Is possible to draw a circle, passing through three points -or residues-? Do you have any suggestions? Thank you for your attention. Have a great week end. Greetings,
Andrea
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
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Andrea Dallapè -
Elaine Meng