From: QT <rdi...@gm...> - 2008-11-10 08:15:11
|
Hello everyone, I have a question regarding camera orientation. I'm using pymol to explore the surface of the peptide tunnel in the ribosome and would like to change the camera orientation so that I can look around "in there" without getting occluded. Clipping plane is not useful because I don't want the surface to disappear. In a sense, I want to change the default camera orientation of pymol from "looking in" to "looking out". This is much like standing in a room and looking around. I think the answer lies in the 18 parameters of set_view, but which should I change and how are these computed? Regards, Quyen Tran Department of Biochemistry University of Houston |
From: DeLano S. <de...@de...> - 2008-11-11 05:15:36
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Quyen, If clipping isn't the effect you want, the solution probably lies in increasing the camera field of view angle which will enable PyMOL to better "get of inside" spaces without having nearby elements appear to intersect the camera surface (or front clipping plane). set field_of_view, 45 Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:su...@de... _____ From: QT [mailto:rdi...@gm...] Sent: Monday, November 10, 2008 12:15 AM To: pym...@li... Subject: [PyMOL] Camera Orientation Hello everyone, I have a question regarding camera orientation. I'm using pymol to explore the surface of the peptide tunnel in the ribosome and would like to change the camera orientation so that I can look around "in there" without getting occluded. Clipping plane is not useful because I don't want the surface to disappear. In a sense, I want to change the default camera orientation of pymol from "looking in" to "looking out". This is much like standing in a room and looking around. I think the answer lies in the 18 parameters of set_view, but which should I change and how are these computed? Regards, Quyen Tran Department of Biochemistry University of Houston |
From: QT <rdi...@gm...> - 2008-11-11 06:04:08
|
Ah thank you Warren, that gave it a fish-eye effect that seems to work. Is there any other way to go about this problem? Is there no way to move the camera from looking in to looking out? By default, the camera is anchored outside the molecule, can the camera be anchored to a point inside the molecule but not on any atom? Quyen On Mon, Nov 10, 2008 at 11:15 PM, DeLano Scientific <de...@de...>wrote: > Quyen, > > If clipping isn't the effect you want, the solution probably lies in > increasing the camera field of view angle which will enable PyMOL to better > "get of inside" spaces without having nearby elements appear to intersect > the camera surface (or front clipping plane). > > set field_of_view, 45 > > Cheers, > Warren > -- > DeLano Scientific LLC > Subscriber Support Services > mailto:su...@de... > > > ------------------------------ > *From:* QT [mailto:rdi...@gm...] > *Sent:* Monday, November 10, 2008 12:15 AM > *To:* pym...@li... > *Subject:* [PyMOL] Camera Orientation > > Hello everyone, > > I have a question regarding camera orientation. I'm using pymol to explore > the surface of the peptide tunnel in the ribosome and would like to change > the camera orientation so that I can look around "in there" without getting > occluded. Clipping plane is not useful because I don't want the surface to > disappear. In a sense, I want to change the default camera orientation of > pymol from "looking in" to "looking out". This is much like standing in a > room and looking around. I think the answer lies in the 18 parameters of > set_view, but which should I change and how are these computed? > > Regards, > Quyen Tran > > Department of Biochemistry > University of Houston > |
From: DeLano S. <de...@de...> - 2008-11-11 06:30:34
|
Ah ha, now I see what you're angling at! What a great question -- I'm amazed this hasn't come up before in ten years of usage and development. The core problem is that PyMOL's camera has been designed from day one to orbit around a specific point in space, not at a point. To get the effect you desire, I think you'll need to transiently back up the camera, rotate it about its prior orgin and then move it back again. Here's an example script which does that: load $TUT/1hpv.pdb set field_of_view, 45 zoom organic orient organic show stick, polymer show surface set surface_color, white set transparency, 0.5 clip slab, 30 set line_width, 5 cmd.move("z",-cmd.get_view()[11]) python def spin(): from pymol import cmd for x in range(360): cmd.move("z",cmd.get_view()[11]) cmd.turn("y",1) cmd.move("z",-cmd.get_view()[11]) cmd.refresh() threading.Thread(target=spin).start() python end Cheers, Warren ________________________________ From: QT [mailto:rdi...@gm...] Sent: Monday, November 10, 2008 10:04 PM To: DeLano Scientific Cc: pym...@li... Subject: Re: [PyMOL] Camera Orientation Ah thank you Warren, that gave it a fish-eye effect that seems to work. Is there any other way to go about this problem? Is there no way to move the camera from looking in to looking out? By default, the camera is anchored outside the molecule, can the camera be anchored to a point inside the molecule but not on any atom? Quyen On Mon, Nov 10, 2008 at 11:15 PM, DeLano Scientific <de...@de...> wrote: Quyen, If clipping isn't the effect you want, the solution probably lies in increasing the camera field of view angle which will enable PyMOL to better "get of inside" spaces without having nearby elements appear to intersect the camera surface (or front clipping plane). set field_of_view, 45 Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:su...@de... ________________________________ From: QT [mailto:rdi...@gm...] Sent: Monday, November 10, 2008 12:15 AM To: pym...@li... Subject: [PyMOL] Camera Orientation Hello everyone, I have a question regarding camera orientation. I'm using pymol to explore the surface of the peptide tunnel in the ribosome and would like to change the camera orientation so that I can look around "in there" without getting occluded. Clipping plane is not useful because I don't want the surface to disappear. In a sense, I want to change the default camera orientation of pymol from "looking in" to "looking out". This is much like standing in a room and looking around. I think the answer lies in the 18 parameters of set_view, but which should I change and how are these computed? Regards, Quyen Tran Department of Biochemistry University of Houston |
From: QT <rdi...@gm...> - 2008-11-11 08:31:07
|
Yup, thanks for your help that did it. Although the script didn't spring back to the default camera anchor point after it did the 360 degree rotation about y-axis, I understand now. So, to move the camera anchor point around, you modify the parameter 9-11 of set_view(), which controls the x,y,z anchor point of the camera. Now I've come to understand that parameter 15 and 16 essentially define the clipping plane. How are these related to each other because I also want to do sectioning of the ribosome tunnel from front to back in 10A increment. Is the clipping plane static or can you also rotate the clipping plane to do horizontal and diagonal sectioning, or is that accomplished by rotating the structure about its axis? By default the clipping plane sections from front to back or vertical sections. Quyen On Tue, Nov 11, 2008 at 12:30 AM, DeLano Scientific <de...@de...>wrote: > Ah ha, now I see what you're angling at! What a great question -- I'm > amazed this hasn't come up before in ten years of usage and development. > > The core problem is that PyMOL's camera has been designed from day one to > orbit around a specific point in space, not at a point. To get the effect > you desire, I think you'll need to transiently back up the camera, rotate > it > about its prior orgin and then move it back again. Here's an example > script > which does that: > > > load $TUT/1hpv.pdb > set field_of_view, 45 > zoom organic > orient organic > show stick, polymer > show surface > set surface_color, white > set transparency, 0.5 > clip slab, 30 > set line_width, 5 > > cmd.move("z",-cmd.get_view()[11]) > > python > > def spin(): > from pymol import cmd > for x in range(360): > cmd.move("z",cmd.get_view()[11]) > cmd.turn("y",1) > cmd.move("z",-cmd.get_view()[11]) > cmd.refresh() > > threading.Thread(target=spin).start() > > python end > > Cheers, > Warren > > > ________________________________ > > From: QT [mailto:rdi...@gm...] > Sent: Monday, November 10, 2008 10:04 PM > To: DeLano Scientific > Cc: pym...@li... > Subject: Re: [PyMOL] Camera Orientation > > > Ah thank you Warren, that gave it a fish-eye effect that seems to work. Is > there any other way to go about this problem? Is there no way to move the > camera from looking in to looking out? By default, the camera is anchored > outside the molecule, can the camera be anchored to a point inside the > molecule but not on any atom? > > Quyen > > > On Mon, Nov 10, 2008 at 11:15 PM, DeLano Scientific <de...@de...> > wrote: > > > Quyen, > > If clipping isn't the effect you want, the solution probably lies in > increasing the camera field of view angle which will enable PyMOL to better > "get of inside" spaces without having nearby elements appear to intersect > the camera surface (or front clipping plane). > > set field_of_view, 45 > > Cheers, > Warren > -- > DeLano Scientific LLC > Subscriber Support Services > mailto:su...@de... > > > ________________________________ > > From: QT [mailto:rdi...@gm...] > Sent: Monday, November 10, 2008 12:15 AM > To: pym...@li... > Subject: [PyMOL] Camera Orientation > > > Hello everyone, > > I have a question regarding camera orientation. I'm using pymol to > explore the surface of the peptide tunnel in the ribosome and would like to > change the camera orientation so that I can look around "in there" without > getting occluded. Clipping plane is not useful because I don't want the > surface to disappear. In a sense, I want to change the default camera > orientation of pymol from "looking in" to "looking out". This is much like > standing in a room and looking around. I think the answer lies in the 18 > parameters of set_view, but which should I change and how are these > computed? > > Regards, > Quyen Tran > > Department of Biochemistry > University of Houston > > > > > |
From: DeLano S. <de...@de...> - 2008-11-11 18:01:30
|
QT, No, unfortunately, it is more complicated than that...see the community wiki: http://pymolwiki.org/index.php/Get_View Also, for sectioning, you may wish to disable depth_cue unset depth_cue Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:su...@de... _____ From: QT [mailto:rdi...@gm...] Sent: Tuesday, November 11, 2008 12:31 AM To: DeLano Scientific Cc: pym...@li... Subject: Re: [PyMOL] Camera Orientation Yup, thanks for your help that did it. Although the script didn't spring back to the default camera anchor point after it did the 360 degree rotation about y-axis, I understand now. So, to move the camera anchor point around, you modify the parameter 9-11 of set_view(), which controls the x,y,z anchor point of the camera. Now I've come to understand that parameter 15 and 16 essentially define the clipping plane. How are these related to each other because I also want to do sectioning of the ribosome tunnel from front to back in 10A increment. Is the clipping plane static or can you also rotate the clipping plane to do horizontal and diagonal sectioning, or is that accomplished by rotating the structure about its axis? By default the clipping plane sections from front to back or vertical sections. Quyen On Tue, Nov 11, 2008 at 12:30 AM, DeLano Scientific <de...@de...> wrote: Ah ha, now I see what you're angling at! What a great question -- I'm amazed this hasn't come up before in ten years of usage and development. The core problem is that PyMOL's camera has been designed from day one to orbit around a specific point in space, not at a point. To get the effect you desire, I think you'll need to transiently back up the camera, rotate it about its prior orgin and then move it back again. Here's an example script which does that: load $TUT/1hpv.pdb set field_of_view, 45 zoom organic orient organic show stick, polymer show surface set surface_color, white set transparency, 0.5 clip slab, 30 set line_width, 5 cmd.move("z",-cmd.get_view()[11]) python def spin(): from pymol import cmd for x in range(360): cmd.move("z",cmd.get_view()[11]) cmd.turn("y",1) cmd.move("z",-cmd.get_view()[11]) cmd.refresh() threading.Thread(target=spin).start() python end Cheers, Warren ________________________________ From: QT [mailto:rdi...@gm...] Sent: Monday, November 10, 2008 10:04 PM To: DeLano Scientific Cc: pym...@li... Subject: Re: [PyMOL] Camera Orientation Ah thank you Warren, that gave it a fish-eye effect that seems to work. Is there any other way to go about this problem? Is there no way to move the camera from looking in to looking out? By default, the camera is anchored outside the molecule, can the camera be anchored to a point inside the molecule but not on any atom? Quyen On Mon, Nov 10, 2008 at 11:15 PM, DeLano Scientific <de...@de...> wrote: Quyen, If clipping isn't the effect you want, the solution probably lies in increasing the camera field of view angle which will enable PyMOL to better "get of inside" spaces without having nearby elements appear to intersect the camera surface (or front clipping plane). set field_of_view, 45 Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:su...@de... ________________________________ From: QT [mailto:rdi...@gm...] Sent: Monday, November 10, 2008 12:15 AM To: pym...@li... Subject: [PyMOL] Camera Orientation Hello everyone, I have a question regarding camera orientation. I'm using pymol to explore the surface of the peptide tunnel in the ribosome and would like to change the camera orientation so that I can look around "in there" without getting occluded. Clipping plane is not useful because I don't want the surface to disappear. In a sense, I want to change the default camera orientation of pymol from "looking in" to "looking out". This is much like standing in a room and looking around. I think the answer lies in the 18 parameters of set_view, but which should I change and how are these computed? Regards, Quyen Tran Department of Biochemistry University of Houston |