[PyMOL] Labels

Hi How can I get my labels to appear in front of a cartoon representation of a protein? Currently I have a decent text size but the text is obscured by the cartoon folding over it. Any help would be appreciated!! Thanks!! -- Tjaart de Beer Bioinformatics and Computational Biology Unit Departm

[PyMOL] cgo cylinders with flat ends? More details

Dear Tsjerk and other pymolites To draw my cylinders I just modified Warren's example from the CGO demos in the examples/devel directory. I give this below. Maybe there is another way to do this? I would like cylindrical cylinders with sharp cut ends rather than rounded ends. I guess this is do

Re: [PyMOL] cgo cylinders with flat ends? More details

Hi Martin, For me (Suse 9.0 Linux, Pymol 0.98b) this scripts seems to do exactly what you want. After rendering that is. If the scene is not rendered, the cylinder is an eight-sided prism, which is due to the openGL implementation. Maybe it would be nice if there would be a setting like cgo_q

Re: [PyMOL] cgo cylinders with flat ends? More details

Dear Tsjerk thanks for that - I am not using the latest pymol so I will upgrade and try again. I will let you know how it goes. cheers Martyn On Wed, 11 May 2005, T.A.Wassenaar wrote: > Date: Wed, 11 May 2005 13:11:54 +0200 > From: T.A.Wasse

[PyMOL] raytracing with depth cue

Dear Pymol users, When I raytrace (using the built-in raytracer) the depth cue disappears. Is there any way to get a high resolution image with depth cue? regards, Anders -- Anders Østergaard Madsen Centre for Crystallographic Studies

Re: [PyMOL] cgo cylinders with flat ends? More details

Dear Tsjerk thanks - you were right - now I have upgraded and they come out as nice flat cylinders, looks good. Thanks again for trying that for me best wishes and regards Martyn > On Wed, 11 May 2005, T.A.Wassenaar wrote: > > > Date: Wed, 11

[PyMOL] raytracing and depth cue

Dear Pymol users, When I raytrace (using the built-in raytracer) the depth cue disappears. Is there any way to get a high resolution (ray traced) image with depth cue? regards, Anders -- Anders Østergaard Madsen Centre for Crystallographic Studies

RE: [PyMOL] cgo cylinders with flat ends? More details

> Maybe it would be nice > if there would be a setting like cgo_quality to enhance such > a view without rendering. makes no sense, but the cgo ylinder quality is bound to stick_quality: set stick_quality, 24 *before* loading the cgo object. Cheers, Warren -- Warren L. DeLano, Ph.D.

RE: [PyMOL] Labels

> How can I get my labels to appear in front of a cartoon > representation of a protein? By making your labels in PowerPoint or Photoshop after rendering in PyMOL. However, thank you for the suggestion -- better labels are a high priority. Cheers, Warren -- Warren L. DeLano, Ph.D.

Re: [PyMOL] raytracing with depth cue

Dear pymol users, I got an answer from several helpful people: I had somehow disabled the depth cue in the raytracing rendering: - There are two settings that give you an impression of depth. depth_cue for the OpenGL display and ray_trace_fog for the ray tracer set ray_trace_fog, 1 to pres

RE: [PyMOL] cgo cylinders with flat ends? More details

Dear Warren thanks for that tip - my cylinders look fine now and render nicely. best wishes and regards, Martyn On Wed, 11 May 2005, Warren DeLano wrote: > Date: Wed, 11 May 2005 07:27:34 -0700 > From: Warren DeLano > To: 'T.A.Wassenaar' , >

[PyMOL] Displaying vectors each frame

Hi - I would like to display some force vectors operating on atoms. These vectors do have a time dependence. I know the general mechanism - create a script which reads the vectors coordinates in and then draws different 3d vector CGOs each frame. Has anyone done this before? any code? Or any p

RE: [PyMOL] Displaying vectors each frame

Thomas, A multi-state CGO object is definitely the way to do with this. Check out the pymol/examples/devel/cgo03.py script for an example of creating just such an object. Cheers, Warren. -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyste

[PyMOL] RE: Crashing PSW files: Likely Solution

PyMOL Users: There have been several reports of crashes when launching PyMOL show (PSW) files (ie. PSE files renamed PSW to trigger the full-screen mode). The common factor behind in these crashes seems to have been Intel Extreme Graphics chips and Windows XP Service Pack 2. We managed to obtain