lost focus wile rotating molecules after zoom-in
I notice that chimera lost focus while rotating molecules after zoom-in operation. Will this problem be solved in the future version? Shawn ___________________________________________________ 您的生活即時通 － 溝通、娛樂、生活、工作一次搞定！ http://messenger.yahoo.com.tw/
I have not seen this problem. Please use chimera's Help / Report a Bug dialog to report the bug so we'll have a record of what version of chimera you're having problems with and what graphics driver version you have and what operating system you're using. With that information, we will try to reproduce your bug and if we can't, we will need to email you and ask a few questions to try and figure out why the bug occurs. Once we can reproduce the bug, we can fix it. Thanks for you help, Greg On Fri, 25 Dec 2009, Sheng-Hung Wang wrote:
I notice that chimera lost focus while rotating molecules after zoom-in operation. Will this problem be solved in the future version?
Shawn
Dear Greg, Sorry for that I did not describe the problem clearly. I'm using ver. 1.4 (build 29251) Chimera running on CentOS 5.x x86_64 Linux. I make a description here first and then I will try to report it through Help dialog. The term "lost focus" I have mentioned means that the centroid of molecule do not always be kept at the center of window. Condition #1. Open a protein structure, and then click FOCUS from ACTIONS of the main menu without selecting anything. After doing zoom-in, rotation, and then zoom-out, the position of molecular centroid migrated. Condition #2. Open a protein and it's ligand in the same session followed by opening MODEL PANEL dialog. Selecting ligand and then focusing it from MODEL PANEL dialog, you will find Chimera do not focus the ligand once molecules are rotated. However, it works fine while selection and focusing are done through main menu. Sincerely, Shawn
I have not seen this problem. Please use chimera's Help / Report a Bug dialog to report the bug so we'll have a record of what version of chimera you're having problems with and what graphics driver version you have and what operating system you're using. With that information, we will try to reproduce your bug and if we can't, we will need to email you and ask a few questions to try and figure out why the bug occurs. Once we can reproduce the bug, we can fix it.
Thanks for you help,
Greg
On Fri, 25 Dec 2009, Sheng-Hung Wang wrote:
I notice that chimera lost focus while rotating molecules after zoom-in operation. Will this problem be solved in the future version?
Shawn
___________________________________________________ 您的生活即時通 － 溝通、娛樂、生活、工作一次搞定！ http://messenger.yahoo.com.tw/
Try updating your chimera to the final 1.4 release, many bugs were found and fixed after the release candidates came out. If you are still having problems, please use chimera's Report a Bug dialog in the Help menu to report the bug. - Greg On Mon, 28 Dec 2009, Sheng-Hung Wang wrote:
Dear Greg,
Sorry for that I did not describe the problem clearly. I'm using ver. 1.4 (build 29251) Chimera running on CentOS 5.x x86_64 Linux. I make a description here first and then I will try to report it through Help dialog. The term "lost focus" I have mentioned means that the centroid of molecule do not always be kept at the center of window. Condition #1. Open a protein structure, and then click FOCUS from ACTIONS of the main menu without selecting anything. After doing zoom-in, rotation, and then zoom-out, the position of molecular centroid migrated. Condition #2. Open a protein and it's ligand in the same session followed by opening MODEL PANEL dialog. Selecting ligand and then focusing it from MODEL PANEL dialog, you will find Chimera do not focus the ligand once molecules are rotated. However, it works fine while selection and focusing are done through main menu. Sincerely, Shawn
I have not seen this problem. Please use chimera's Help / Report a Bug dialog to report the bug so we'll have a record of what version of chimera you're having problems with and what graphics driver version you have and what operating system you're using. With that information, we will try to reproduce your bug and if we can't, we will need to email you and ask a few questions to try and figure out why the bug occurs. Once we can reproduce the bug, we can fix it.
Thanks for you help,
Greg
On Fri, 25 Dec 2009, Sheng-Hung Wang wrote:
I notice that chimera lost focus while rotating molecules after zoom-in operation. Will this problem be solved in the future version?
Shawn
___________________________________________________ 您的生活即時通 － 溝通、娛樂、生活、工作一次搞定！ http://messenger.yahoo.com.tw/ _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Shawn, Your case #1 is normal Chimera 1.4 behavior as described in the documentation: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sideview.html#rotation "center of rotation method: front center (default) - when the view is zoomed out, behaves like center of models; when the view is zoomed in on parts of items, behaves like center of view, except the center of rotation depth (Z-coordinate) is set to that of the frontmost displayed unclipped atom whose VDW sphere intercepts a line perpendicular to the screen in the window center. The center is not updated when only rotations are performed. " If you prefer the Chimera 1.3 behavior where rotation is about the center of the molecule even when you are zoomed in then set the rotation center to "center of models" and save that setting for future sessions. Details are on the above web page. For case #2 that is a bug with the Model Panel dialog Focus button in Chimera 1.4 and I'll look at it shortly. http://plato.cgl.ucsf.edu/trac/chimera/ticket/8036 Tom -------- Original Message -------- Subject: Re: [Chimera-users] lost focus wile rotating molecules after zoom-in From: Sheng-Hung Wang To: chimera-users Date: 12/27/09 7:02 PM
Dear Greg,
Sorry for that I did not describe the problem clearly. I'm using ver. 1.4 (build 29251) Chimera running on CentOS 5.x x86_64 Linux. I make a description here first and then I will try to report it through Help dialog. The term "lost focus" I have mentioned means that the centroid of molecule do not always be kept at the center of window.
Condition #1. Open a protein structure, and then click FOCUS from ACTIONS of the main menu without selecting anything. After doing zoom-in, rotation, and then zoom-out, the position of molecular centroid migrated.
Condition #2. Open a protein and it's ligand in the same session followed by opening MODEL PANEL dialog. Selecting ligand and then focusing it from MODEL PANEL dialog, you will find Chimera do not focus the ligand once molecules are rotated. However, it works fine while selection and focusing are done through main menu.
Sincerely, Shawn
On Jan 4, 2010, at 12:04 PM, Thomas Goddard wrote:
Condition #2. Open a protein and it's ligand in the same session followed by opening MODEL PANEL dialog. Selecting ligand and then focusing it from MODEL PANEL dialog, you will find Chimera do not focus the ligand once molecules are rotated. However, it works fine while selection and focusing are done through main menu.
"Focus" in the Model Panel focuses on the chosen model(s), not on the selection. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Hi Eric, The Model Panel Focus button does seem to be broken. The case I tested was 3F5P with just chain A and ligand deleted as one model, and 3F5P just chain A with non-ligand deleted -- two models. Highlighting just the ligand model in Model Panel and pressing Focus in the Model Panel and then rotating soon sends the ligand out of view. The command "focus #1" (model 1 is the ligand) works correctly. Tom -------- Original Message -------- Subject: Re: [Chimera-users] lost focus wile rotating molecules after zoom-in From: Eric Pettersen <pett@cgl.ucsf.edu> To: Thomas Goddard <goddard@cgl.ucsf.edu> Date: 1/4/10 1:56 PM
On Jan 4, 2010, at 12:04 PM, Thomas Goddard wrote:
Condition #2. Open a protein and it's ligand in the same session followed by opening MODEL PANEL dialog. Selecting ligand and then focusing it from MODEL PANEL dialog, you will find Chimera do not focus the ligand once molecules are rotated. However, it works fine while selection and focusing are done through main menu.
"Focus" in the Model Panel focuses on the chosen model(s), not on the selection.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Dear Tom, I see! I greatly appreciate Chimera team!
Hi Shawn,
Your case #1 is normal Chimera 1.4 behavior as described in the documentation:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sideview.html#rotation
"center of rotation method:
front center (default) - when the view is zoomed out, behaves like center of models; when the view is zoomed in on parts of items, behaves like center of view, except the center of rotation depth (Z-coordinate) is set to that of the frontmost displayed unclipped atom whose VDW sphere intercepts a line perpendicular to the screen in the window center. The center is not updated when only rotations are performed. "
If you prefer the Chimera 1.3 behavior where rotation is about the center of the molecule even when you are zoomed in then set the rotation center to "center of models" and save that setting for future sessions. Details are on the above web page.
For case #2 that is a bug with the Model Panel dialog Focus button in Chimera 1.4 and I'll look at it shortly.
http://plato.cgl.ucsf.edu/trac/chimera/ticket/8036
Tom
-------- Original Message -------- Subject: Re: [Chimera-users] lost focus wile rotating molecules after zoom-in From: Sheng-Hung Wang To: chimera-users Date: 12/27/09 7:02 PM
Dear Greg,
Sorry for that I did not describe the problem clearly. I'm using ver. 1.4 (build 29251) Chimera running on CentOS 5.x x86_64 Linux. I make a description here first and then I will try to report it through Help dialog. The term "lost focus" I have mentioned means that the centroid of molecule do not always be kept at the center of window. Condition #1. Open a protein structure, and then click FOCUS from ACTIONS of the main menu without selecting anything. After doing zoom-in, rotation, and then zoom-out, the position of molecular centroid migrated.
Condition #2. Open a protein and it's ligand in the same session followed by opening MODEL PANEL dialog. Selecting ligand and then focusing it from MODEL PANEL dialog, you will find Chimera do not focus the ligand once molecules are rotated. However, it works fine while selection and focusing are done through main menu.
Sincerely, Shawn
___________________________________________________ 您的生活即時通 － 溝通、娛樂、生活、工作一次搞定！ http://messenger.yahoo.com.tw/
participants (4)
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Eric Pettersen -
Greg Couch -
Sheng-Hung Wang -
Thomas Goddard