[PyMOL] Questions & comments about CGO objects

2005-05-30 Thread Grégori Gerebtzoff
Hi list !

I was just building (successfully) my first CGO object, and I have three
questions and two comment:

 

Questions:

1) what is the difference between LINES, LINE_LOOP, LINE_STRIP. If I
understood correctly, LINES is to build single lines,

LINE_LOOP will connect the first and the last point (VERTEX), but no clue
about LINE_STRIP.

2) what is the difference between TRIANGLES, TRIANGLES_STRIP and
TRIANGLE_FAN

3) is it possible to render a plain polygon (I suppose I can build a
succession of triangles, but is there another way to do it?)

 

Comments:

1) in the Pymol manual, I read that LINEWIDTH was for… line-width, and
WIDTHSCALE was for ray-tracing;

but what I observed is that LINEWIDTH do not change the line thickness
(always 1 pixel) in the normal view but in ray-traced images,
and when I use WIDTHSCALE Pymol simply crashes during ray-tracing… Is this a
bug? I use the latest version of Pymol with 
WinXP Pro SP2 and my graphic card is an ATI Radeon 9700 with the latest
drivers.

2) when you use the COLOR command in a CGO object, this color cannot be
overridden with the color menu in Pymol, so simply

don’t use the COLOR command if you want to be able to change the color of
your object within Pymol!

 

Many thanks for your answer(s)!

 

 

Grégori Gerebtzoff

 

Division of Biophysical Chemistry

Biozentrum, University of Basel

Klingelbergstrasse 70

CH-4056 Basel / Switzerland

 

Tel: +41 61 267 21 92

Fax: +41 61 267 21 89

e-mail: gregori.gerebtz...@unibas.ch



RE: [PyMOL] transparency surface

2005-05-30 Thread Grégori Gerebtzoff
Simply type

show surface
set transparency=0.5, my_object


This syntax is true for most Pymol commands...

Greg





RE: [PyMOL] Questions & comments about CGO objects

2005-05-30 Thread Warren DeLano
Gergori,

> 1) what is the difference between LINES, LINE_LOOP, 
> LINE_STRIP. If I understood correctly, LINES is to build single lines,
> 
> LINE_LOOP will connect the first and the last point (VERTEX), 
> but no clue about LINE_STRIP.
> 
> 2) what is the difference between TRIANGLES, TRIANGLES_STRIP 
> and TRIANGLE_FAN

Consult OpenGL docs (GL_LINES, GL_LINE_LOOP, etc.) -- CGOs are essentially
just OpenGL rendering streams.
 
> 3) is it possible to render a plain polygon (I suppose I can 
> build a succession of triangles, but is there another way to do it?)

Not with CGOs.  The ray tracer only has triangle, cylinder, and spheres
primitives, which is why CGOs are limited to just triangles, spheres, and
cylinders.

> 1) in the Pymol manual, I read that LINEWIDTH was for… 
> line-width, and WIDTHSCALE was for ray-tracing;
> but what I observed is that LINEWIDTH do not change the line 
> thickness (always 1 pixel) in the normal view but in 
> ray-traced images, and when I use WIDTHSCALE Pymol simply 
> crashes during ray-tracing… Is this a bug? I use the latest 
> version of Pymol with WinXP Pro SP2 and my graphic card is an 
> ATI Radeon 9700 with the latest drivers.

Not sture, but I think WIDTHSCALE is basically broken and should be
deprecated.  LINEWIDTH should work, but if it doesn’t, then I suggest using
the  cgo_line_width setting to control line widths for now.

Cheers,
Warren

--
Warren L. DeLano, Ph.D. 
Principal Scientist

. DeLano Scientific LLC  
. 400 Oyster Point Blvd., Suite 213   
. South San Francisco, CA 94080 USA   
. Biz:(650)-872-0942  Tech:(650)-872-0834 
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:war...@delsci.com  
 

> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net 
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
> Grégori Gerebtzoff
> Sent: Monday, May 30, 2005 6:08 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Questions & comments about CGO objects
> 
> Hi list !
> 
> I was just building (successfully) my first CGO object, and I 
> have three questions and two comment:
> 
>  
> 
> Questions:
> 
> 1) what is the difference between LINES, LINE_LOOP, 
> LINE_STRIP. If I understood correctly, LINES is to build single lines,
> 
> LINE_LOOP will connect the first and the last point (VERTEX), 
> but no clue about LINE_STRIP.
> 
> 2) what is the difference between TRIANGLES, TRIANGLES_STRIP 
> and TRIANGLE_FAN
> 
> 3) is it possible to render a plain polygon (I suppose I can 
> build a succession of triangles, but is there another way to do it?)
> 
>  
> 
> Comments:
> 
> 1) in the Pymol manual, I read that LINEWIDTH was for… 
> line-width, and WIDTHSCALE was for ray-tracing;
> 
> but what I observed is that LINEWIDTH do not change the line 
> thickness (always 1 pixel) in the normal view but in 
> ray-traced images, and when I use WIDTHSCALE Pymol simply 
> crashes during ray-tracing… Is this a bug? I use the latest 
> version of Pymol with WinXP Pro SP2 and my graphic card is an 
> ATI Radeon 9700 with the latest drivers.
> 
> 2) when you use the COLOR command in a CGO object, this color 
> cannot be overridden with the color menu in Pymol, so simply
> 
> don’t use the COLOR command if you want to be able to change 
> the color of your object within Pymol!
> 
>  
> 
> Many thanks for your answer(s)!
> 
>  
> 
>  
> 
> Grégori Gerebtzoff
> 
>  
> 
> Division of Biophysical Chemistry
> 
> Biozentrum, University of Basel
> 
> Klingelbergstrasse 70
> 
> CH-4056 Basel / Switzerland
> 
>  
> 
> Tel: +41 61 267 21 92
> 
> Fax: +41 61 267 21 89
> 
> e-mail: gregori.gerebtz...@unibas.ch
> 
>