I asked this question several months ago, but rarely have applied the answer. I have a structure that has a long stretch that is disordered. In the structure it appears as a dashed line. If I highlight this section of the total sequence and then apply a color (red) the whole structure is then colored red. So how can I make the dashes slightly larger, and secondly color that stretch of dashes with a particular color without coloring the rest of the molecule? Thank you Arthur G. Szabo
Hi Arthur, First Ctrl-click on the dashed line to select it. Then, click the green magnifying glass icon near the bottom right of the Chimera window to open the Selection Inspector. In the Inspector window (Inspect: Pseudobond): (1) change “halfbond mode” to “off”, otherwise it will get colored by the atoms instead of having its own color (2) click or doubleclick the square color thing to make the Color Editor window appear, in which you can change the color To make the dashed line fatter, stay in the Inspector tool but now use pulldown menu to Inspect: Pseudobond group (instead of just Inspect: Pseudobond), then: change “line width” to some bigger number I hope this helps, 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 Apr 28, 2017, at 12:16 PM, Arthur Szabo <agszabo@outlook.com> wrote:
I asked this question several months ago, but rarely have applied the answer. I have a structure that has a long stretch that is disordered. In the structure it appears as a dashed line. If I highlight this section of the total sequence and then apply a color (red) the whole structure is then colored red.
So how can I make the dashes slightly larger, and secondly color that stretch of dashes with a particular color without coloring the rest of the molecule? Thank you Arthur G. Szabo
Elaine Thank you for your usual prompt reply. Will try it. Thanks arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Friday, April 28, 2017 3:52 PM To: Arthur Szabo <agszabo@outlook.com> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] assistance changing pseudobond appearance Hi Arthur, First Ctrl-click on the dashed line to select it. Then, click the green magnifying glass icon near the bottom right of the Chimera window to open the Selection Inspector. In the Inspector window (Inspect: Pseudobond): (1) change “halfbond mode” to “off”, otherwise it will get colored by the atoms instead of having its own color (2) click or doubleclick the square color thing to make the Color Editor window appear, in which you can change the color To make the dashed line fatter, stay in the Inspector tool but now use pulldown menu to Inspect: Pseudobond group (instead of just Inspect: Pseudobond), then: change “line width” to some bigger number I hope this helps, 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 Apr 28, 2017, at 12:16 PM, Arthur Szabo <agszabo@outlook.com> wrote:
I asked this question several months ago, but rarely have applied the answer. I have a structure that has a long stretch that is disordered. In the structure it appears as a dashed line. If I highlight this section of the total sequence and then apply a color (red) the whole structure is then colored red.
So how can I make the dashes slightly larger, and secondly color that stretch of dashes with a particular color without coloring the rest of the molecule? Thank you Arthur G. Szabo
Elaine My response on Friday was probably premature. I followed your instructions and I appeared to have been able to highlight (select) the dashed line that represented the disordered residues. In the Selection Inspector with Pseudobond in the Inspect window, I turned the "halfbond" mode to "off" and double clicked on color, and selected a color "red". I then used the pulldown menu and selected Inspect Pseudobond group. The color was not what I selected previously so I reselected the color red in that square. I changed the width to 3.0. The width and color within the green selection envelope appears to be correct. Now the problem: Which button do I select on the bottom of that Selection Inspector window. If I click on "close" then the dashed line disappears. Strangely if I rotate the image I can sometimes see it , but it is very hard to set the rotational position where the dashed line is visible. Alternately if I go to select on the main menu, and click on clear selection the dashed line totally disappears. So I appear to be stuck. Not sure if clicking on "close" on the Selection Inspector was the right thing to do. Thanks arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Friday, April 28, 2017 3:52 PM To: Arthur Szabo <agszabo@outlook.com> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] assistance changing pseudobond appearance Hi Arthur, First Ctrl-click on the dashed line to select it. Then, click the green magnifying glass icon near the bottom right of the Chimera window to open the Selection Inspector. In the Inspector window (Inspect: Pseudobond): (1) change “halfbond mode” to “off”, otherwise it will get colored by the atoms instead of having its own color (2) click or doubleclick the square color thing to make the Color Editor window appear, in which you can change the color To make the dashed line fatter, stay in the Inspector tool but now use pulldown menu to Inspect: Pseudobond group (instead of just Inspect: Pseudobond), then: change “line width” to some bigger number I hope this helps, 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 Apr 28, 2017, at 12:16 PM, Arthur Szabo <agszabo@outlook.com> wrote:
I asked this question several months ago, but rarely have applied the answer. I have a structure that has a long stretch that is disordered. In the structure it appears as a dashed line. If I highlight this section of the total sequence and then apply a color (red) the whole structure is then colored red.
So how can I make the dashes slightly larger, and secondly color that stretch of dashes with a particular color without coloring the rest of the molecule? Thank you Arthur G. Szabo
Hi Arthur, You do not need to change color for “Pseudobond group” if changing the “Pseudobond” color already shows what you want in the main window. The individual color overrides the group color. Closing the Selection Inspector should not have any effect on what is shown in the main window. It sounds like a rendering problem on your computer, such as needing to update the graphics driver or install a better graphics driver. You could try clearing the selection (e.g. Ctrl-click in empty space) and seeing if that makes the line reappear. If you saved the session you could try restoring it and seeing if your line reappears. Then if you have to change the line again, just try clearing the selection before closing the Selection Inspector to see if that makes it behave any better. However, you did not do anything wrong and the problem is not within Chimera… this would just be playing around to try to avoid the mysterious behavior. I don’t have any definitive answer, not knowing the specific cause, sorry. 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 May 1, 2017, at 10:15 AM, Arthur Szabo <agszabo@outlook.com> wrote:
Elaine
My response on Friday was probably premature.
I followed your instructions and I appeared to have been able to highlight (select) the dashed line that represented the disordered residues. In the Selection Inspector with Pseudobond in the Inspect window, I turned the "halfbond" mode to "off" and double clicked on color, and selected a color "red". I then used the pulldown menu and selected Inspect Pseudobond group. The color was not what I selected previously so I reselected the color red in that square. I changed the width to 3.0. The width and color within the green selection envelope appears to be correct.
Now the problem: Which button do I select on the bottom of that Selection Inspector window. If I click on "close" then the dashed line disappears. Strangely if I rotate the image I can sometimes see it , but it is very hard to set the rotational position where the dashed line is visible.
Alternately if I go to select on the main menu, and click on clear selection the dashed line totally disappears.
So I appear to be stuck. Not sure if clicking on "close" on the Selection Inspector was the right thing to do.
Thanks
arthur
Another thing to make sure is that when you choose the color, do not make it 100% transparent. It could have happened by mistake if you are showing the “A” line in the Color Editor and set its value to 0 (zero opacity, same as 100% transparent). See Color Editor figure. The “A” line is shown when you check the “Opacity” option. If you weren’t showing it, however, that is not the problem. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/colortool.html>
On May 1, 2017, at 10:44 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Arthur, You do not need to change color for “Pseudobond group” if changing the “Pseudobond” color already shows what you want in the main window. The individual color overrides the group color.
Closing the Selection Inspector should not have any effect on what is shown in the main window. It sounds like a rendering problem on your computer, such as needing to update the graphics driver or install a better graphics driver. You could try clearing the selection (e.g. Ctrl-click in empty space) and seeing if that makes the line reappear. If you saved the session you could try restoring it and seeing if your line reappears. Then if you have to change the line again, just try clearing the selection before closing the Selection Inspector to see if that makes it behave any better. However, you did not do anything wrong and the problem is not within Chimera… this would just be playing around to try to avoid the mysterious behavior. I don’t have any definitive answer, not knowing the specific cause, sorry. 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 May 1, 2017, at 10:15 AM, Arthur Szabo <agszabo@outlook.com> wrote:
Elaine
My response on Friday was probably premature.
I followed your instructions and I appeared to have been able to highlight (select) the dashed line that represented the disordered residues. In the Selection Inspector with Pseudobond in the Inspect window, I turned the "halfbond" mode to "off" and double clicked on color, and selected a color "red". I then used the pulldown menu and selected Inspect Pseudobond group. The color was not what I selected previously so I reselected the color red in that square. I changed the width to 3.0. The width and color within the green selection envelope appears to be correct.
Now the problem: Which button do I select on the bottom of that Selection Inspector window. If I click on "close" then the dashed line disappears. Strangely if I rotate the image I can sometimes see it , but it is very hard to set the rotational position where the dashed line is visible.
Alternately if I go to select on the main menu, and click on clear selection the dashed line totally disappears.
So I appear to be stuck. Not sure if clicking on "close" on the Selection Inspector was the right thing to do.
Thanks
arthur
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Elaine Thank you for your suggestions, but I did not click on the opacity button. In the Selection Inspector, I have been able to select the color of the disordered sequence and there is no issue visualizing it at any rotation. Furthermore its color is not influenced by the color of the adjacent ordered segments. It is when I try to change the line thickness using Pseudbond Group that the dashed line disappears. Either closing the Selection Inspector or clearing the selection causes the series of dashes to disappear. When I control click on a blank part of the screen the dashed line is not restored. I can rotate the structure and at certain positions the dashedline reappears but only a certain specific rotations. Thanks for your assistance once again. I can live with the narrow set of red colored dashes. Arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Monday, May 01, 2017 1:50 PM To: Arthur Szabo <agszabo@outlook.com> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] assistance changing pseudobond appearance Another thing to make sure is that when you choose the color, do not make it 100% transparent. It could have happened by mistake if you are showing the “A” line in the Color Editor and set its value to 0 (zero opacity, same as 100% transparent). See Color Editor figure. The “A” line is shown when you check the “Opacity” option. If you weren’t showing it, however, that is not the problem. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/colortool.html>
On May 1, 2017, at 10:44 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Arthur, You do not need to change color for “Pseudobond group” if changing the “Pseudobond” color already shows what you want in the main window. The individual color overrides the group color.
Closing the Selection Inspector should not have any effect on what is shown in the main window. It sounds like a rendering problem on your computer, such as needing to update the graphics driver or install a better graphics driver. You could try clearing the selection (e.g. Ctrl-click in empty space) and seeing if that makes the line reappear. If you saved the session you could try restoring it and seeing if your line reappears. Then if you have to change the line again, just try clearing the selection before closing the Selection Inspector to see if that makes it behave any better. However, you did not do anything wrong and the problem is not within Chimera… this would just be playing around to try to avoid the mysterious behavior. I don’t have any definitive answer, not knowing the specific cause, sorry. 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 May 1, 2017, at 10:15 AM, Arthur Szabo <agszabo@outlook.com> wrote:
Elaine
My response on Friday was probably premature.
I followed your instructions and I appeared to have been able to highlight (select) the dashed line that represented the disordered residues. In the Selection Inspector with Pseudobond in the Inspect window, I turned the "halfbond" mode to "off" and double clicked on color, and selected a color "red". I then used the pulldown menu and selected Inspect Pseudobond group. The color was not what I selected previously so I reselected the color red in that square. I changed the width to 3.0. The width and color within the green selection envelope appears to be correct.
Now the problem: Which button do I select on the bottom of that Selection Inspector window. If I click on "close" then the dashed line disappears. Strangely if I rotate the image I can sometimes see it , but it is very hard to set the rotational position where the dashed line is visible.
Alternately if I go to select on the main menu, and click on clear selection the dashed line totally disappears.
So I appear to be stuck. Not sure if clicking on "close" on the Selection Inspector was the right thing to do.
Thanks
arthur
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Definitely sounds like a graphics-driver type of problem. Maybe it would work with linewidth 2 instead of 3, but I really don’t know. Elaine P.S. Similar problem reported last year... <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-April/012193.html> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-April/012196.html>
On May 1, 2017, at 11:29 AM, Arthur Szabo <agszabo@outlook.com> wrote:
Elaine
Thank you for your suggestions, but I did not click on the opacity button.
In the Selection Inspector, I have been able to select the color of the disordered sequence and there is no issue visualizing it at any rotation. Furthermore its color is not influenced by the color of the adjacent ordered segments.
It is when I try to change the line thickness using Pseudbond Group that the dashed line disappears. Either closing the Selection Inspector or clearing the selection causes the series of dashes to disappear. When I control click on a blank part of the screen the dashed line is not restored. I can rotate the structure and at certain positions the dashedline reappears but only a certain specific rotations.
Thanks for your assistance once again. I can live with the narrow set of red colored dashes.
Arthur
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Monday, May 01, 2017 1:50 PM To: Arthur Szabo <agszabo@outlook.com> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] assistance changing pseudobond appearance
Another thing to make sure is that when you choose the color, do not make it 100% transparent. It could have happened by mistake if you are showing the “A” line in the Color Editor and set its value to 0 (zero opacity, same as 100% transparent).
See Color Editor figure. The “A” line is shown when you check the “Opacity” option. If you weren’t showing it, however, that is not the problem. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/colortool.html>
On May 1, 2017, at 10:44 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Arthur, You do not need to change color for “Pseudobond group” if changing the “Pseudobond” color already shows what you want in the main window. The individual color overrides the group color.
Closing the Selection Inspector should not have any effect on what is shown in the main window. It sounds like a rendering problem on your computer, such as needing to update the graphics driver or install a better graphics driver. You could try clearing the selection (e.g. Ctrl-click in empty space) and seeing if that makes the line reappear. If you saved the session you could try restoring it and seeing if your line reappears. Then if you have to change the line again, just try clearing the selection before closing the Selection Inspector to see if that makes it behave any better. However, you did not do anything wrong and the problem is not within Chimera… this would just be playing around to try to avoid the mysterious behavior. I don’t have any definitive answer, not knowing the specific cause, sorry. 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 May 1, 2017, at 10:15 AM, Arthur Szabo <agszabo@outlook.com> wrote:
Elaine
My response on Friday was probably premature.
I followed your instructions and I appeared to have been able to highlight (select) the dashed line that represented the disordered residues. In the Selection Inspector with Pseudobond in the Inspect window, I turned the "halfbond" mode to "off" and double clicked on color, and selected a color "red". I then used the pulldown menu and selected Inspect Pseudobond group. The color was not what I selected previously so I reselected the color red in that square. I changed the width to 3.0. The width and color within the green selection envelope appears to be correct.
Now the problem: Which button do I select on the bottom of that Selection Inspector window. If I click on "close" then the dashed line disappears. Strangely if I rotate the image I can sometimes see it , but it is very hard to set the rotational position where the dashed line is visible.
Alternately if I go to select on the main menu, and click on clear selection the dashed line totally disappears.
So I appear to be stuck. Not sure if clicking on "close" on the Selection Inspector was the right thing to do.
Thanks
arthur
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Elaine Sorted the problem out. Selection Inspector doesn't like going above 2.0 when using dashes to represent a disordered structure. Thanks for your help arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Monday, May 01, 2017 2:36 PM To: Arthur Szabo <agszabo@outlook.com> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] assistance changing pseudobond appearance Definitely sounds like a graphics-driver type of problem. Maybe it would work with linewidth 2 instead of 3, but I really don’t know. Elaine P.S. Similar problem reported last year... <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-April/012193.html> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-April/012196.html>
On May 1, 2017, at 11:29 AM, Arthur Szabo <agszabo@outlook.com> wrote:
Elaine
Thank you for your suggestions, but I did not click on the opacity button.
In the Selection Inspector, I have been able to select the color of the disordered sequence and there is no issue visualizing it at any rotation. Furthermore its color is not influenced by the color of the adjacent ordered segments.
It is when I try to change the line thickness using Pseudbond Group that the dashed line disappears. Either closing the Selection Inspector or clearing the selection causes the series of dashes to disappear. When I control click on a blank part of the screen the dashed line is not restored. I can rotate the structure and at certain positions the dashedline reappears but only a certain specific rotations.
Thanks for your assistance once again. I can live with the narrow set of red colored dashes.
Arthur
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Monday, May 01, 2017 1:50 PM To: Arthur Szabo <agszabo@outlook.com> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] assistance changing pseudobond appearance
Another thing to make sure is that when you choose the color, do not make it 100% transparent. It could have happened by mistake if you are showing the “A” line in the Color Editor and set its value to 0 (zero opacity, same as 100% transparent).
See Color Editor figure. The “A” line is shown when you check the “Opacity” option. If you weren’t showing it, however, that is not the problem. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/colortool.html>
On May 1, 2017, at 10:44 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Arthur, You do not need to change color for “Pseudobond group” if changing the “Pseudobond” color already shows what you want in the main window. The individual color overrides the group color.
Closing the Selection Inspector should not have any effect on what is shown in the main window. It sounds like a rendering problem on your computer, such as needing to update the graphics driver or install a better graphics driver. You could try clearing the selection (e.g. Ctrl-click in empty space) and seeing if that makes the line reappear. If you saved the session you could try restoring it and seeing if your line reappears. Then if you have to change the line again, just try clearing the selection before closing the Selection Inspector to see if that makes it behave any better. However, you did not do anything wrong and the problem is not within Chimera… this would just be playing around to try to avoid the mysterious behavior. I don’t have any definitive answer, not knowing the specific cause, sorry. 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 May 1, 2017, at 10:15 AM, Arthur Szabo <agszabo@outlook.com> wrote:
Elaine
My response on Friday was probably premature.
I followed your instructions and I appeared to have been able to highlight (select) the dashed line that represented the disordered residues. In the Selection Inspector with Pseudobond in the Inspect window, I turned the "halfbond" mode to "off" and double clicked on color, and selected a color "red". I then used the pulldown menu and selected Inspect Pseudobond group. The color was not what I selected previously so I reselected the color red in that square. I changed the width to 3.0. The width and color within the green selection envelope appears to be correct.
Now the problem: Which button do I select on the bottom of that Selection Inspector window. If I click on "close" then the dashed line disappears. Strangely if I rotate the image I can sometimes see it , but it is very hard to set the rotational position where the dashed line is visible.
Alternately if I go to select on the main menu, and click on clear selection the dashed line totally disappears.
So I appear to be stuck. Not sure if clicking on "close" on the Selection Inspector was the right thing to do.
Thanks
arthur
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Arthur Szabo -
Elaine Meng