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

[Tobias Beck]

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 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  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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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>
>
>  
> This email message, including any attachments, is for the sole use of the
> intended recipient(s) and may contain information that is proprietary,
> confidential, and exempt from disclosure under applicable law. Any
> unauthorized review, use, disclosure, or distribution is prohibited. If you
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> and delete the original message. Please note, the recipient should check
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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
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Re: [PyMOL] Ligand surface: color issue after ray

[Sampson, Jared]

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 
mailto:tobiasb...@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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This email message, including any attachments, is for the sole use of the 
intended recipient(s) and may contain information that is proprietary, 
confidential, and exempt from disclosure under applicable law. Any unauthorized 
review, use, disclosure, or distribution is prohibited. If you have received 
this email in error please notify the sender by return email and delete the 
original message. Please note, the recipient should check this email and any 
attachments for the presence of viruses. The organization accepts no liability 
for any damage caused by any virus transmitted by this email.
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[PyMOL] Ligand surface: color issue after ray

[Tobias Beck]

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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