Re: [PyMOL] Ligand surface: color issue after ray

[Tobias B. <tob...@gm...>]

Hi Jared,

Thanks a lot for your help and fast response!

Next time I will try to do it as you described, without creating a new
object, but for now hiding the sticks for the surface object did the job!

Thanks again!

Best wishes, Tobias.


On Mon, Mar 31, 2014 at 9:33 PM, Sampson, Jared <Jar...@ny...>wrote:

>  Hi Tobias -
>
>  It seems to me that you may not have hidden the lines/sticks from the
> object where you've shown the surface. For overlapping objects, the normal
> non-ray-traced view appears to give precedence to the object that was
> present in the viewer first.  Try disabling and re-enabling your two
> objects in different orders to see what I mean.  Ray, on the other hand,
> tries to show both at the same time.
>
>  There is actually another way to accomplish what you describe in (b).
>  First, you can use the `surface_mode` setting (
> http://pymolwiki.org/index.php/Surface_mode) to avoid having to modify
> the flags.  Also, instead of creating two objects, the easiest way to have
> different colors for the surface and the sticks is to use the
> `surface_color` setting (http://pymolwiki.org/index.php/Surface_color)
> for your ligand object.
>
>  set surface_mode, 1
> set transparency, 0.5
> as sticks, ligand
> show surface, ligand
> set surface_color, black, ligand
>
>  Hope that helps.
>
>  Cheers,
> Jared
>
>  --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> 550 First Avenue
> New York, NY 10016
> 212-263-7898
> http://kong.med.nyu.edu/
>
>
>
>  On Mar 31, 2014, at 8:42 AM, Tobias Beck <tob...@gm...> wrote:
>
>      Dear all,
>
>  I would like to show a transparent surface of a ligand, with the ligand
> 'inside' as sticks.
>
>  I created a new object of the ligand, then tried to show the surface,
> which fails.
>
> With this information here:
> http://sourceforge.net/p/pymol/mailman/message/27299068/
>
> # do not ignore surfacing of ligands
>
> flag ignore, not rep surface
>
> # force PyMOL to rebuild the surface
>
> rebuild
>
>  I was then able to show the surface of the ligand. All colors are fine.
> Transparency is set to 0.5
>
>  Now I would like to create an image with ray. However, after ray, there
> are problems with the color of the ligand sticks inside:
>
>  a) if the ligand is green and the surface is black, the ligand sticks
> inside are black as well
>
>  b) if the surface is black and the ligand carbon atoms are shown in green
> and other atoms colored by 'color by element', then the non-carbon atoms
> have their native color with pixels of black (surface color) covering
> them....
>
> I would like to get b) to work. Any suggestions? Do the commands above
> (flag ignore) change something for ray?
>
>  For other surfaces (protein), the above works fine, without any pixels of
> surface color on the non-carbon atoms.
>
>  Thank you and best wishes, Tobias.
>
> --
> _______________________________________
>
> Dr. Tobias Beck
> ETH Zurich
> Laboratory of Organic Chemistry
> Vladimir-Prelog-Weg 3, HCI F 322
> 8093 Zurich, Switzerland
> phone:  +41 44 632 68 65
> fax:        +41 44 632 14 86
> web:      http://www.protein.ethz.ch/people/tobias
> _______________________________________
>
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-- 
_______________________________________

Dr. Tobias Beck
ETH Zurich
Laboratory of Organic Chemistry
Vladimir-Prelog-Weg 3, HCI F 322
8093 Zurich, Switzerland
phone:  +41 44 632 68 65
fax:        +41 44 632 14 86
web:      http://www.protein.ethz.ch/people/tobias
_______________________________________