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 <Jared.Sampson@nyumc.org> 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 <tobiasbeck@gmail.com> 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
_______________________________________