Re: [PyMOL] Cartoon_transparency

[Criss Hartzell]

Transparency mode solves it. Thanks.

On Sat, May 8, 2021 at 2:41 PM Jarrett Johnson <
jarrett.john...@schrodinger.com> wrote:

> Hi Criss,
>
> It doesn't appear to be broken from what I see. Helices may not appear
> transparent to each other if you're using single-layer transparency by
> default. Setting `transparency_mode` to 3 should show transparent objects
> beneath each other.
>
> https://pymolwiki.org/index.php/Transparency_mode
>
> Best,
>
> Jarrett J
>
> On Sat, May 8, 2021 at 10:01 AM Criss Hartzell 
> wrote:
>
>> I am using PYMOL2.4.1 on windows.
>> I want to make two cartoon helices transparent in an object having 10
>> heleices. Before version 2.3, I would make a copy of the object, hide the
>> two transparent helices on the original object and show them on the copy
>> with transparency set to 0.5. After PYMOL2.3, cartoon-transparency is
>> supposed to work on the atom level, but when I try to apply cartoon
>> transparency to the two helices as a selection
>> (cartoon_transparency,0.5,sele), the helices change color but do not become
>> transparent. Am I doing something wrong?
>>
>> --
>> Criss Hartzell
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>
>
>
> --
>
> *Jarrett Johnson* | Senior Developer
> [image: Schrodinger Logo] 
>


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Criss Hartzell
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Re: [PyMOL] Cartoon_transparency

[Jarrett Johnson]

Hi Criss,

It doesn't appear to be broken from what I see. Helices may not appear
transparent to each other if you're using single-layer transparency by
default. Setting `transparency_mode` to 3 should show transparent objects
beneath each other.

https://pymolwiki.org/index.php/Transparency_mode

Best,

Jarrett J

On Sat, May 8, 2021 at 10:01 AM Criss Hartzell 
wrote:

> I am using PYMOL2.4.1 on windows.
> I want to make two cartoon helices transparent in an object having 10
> heleices. Before version 2.3, I would make a copy of the object, hide the
> two transparent helices on the original object and show them on the copy
> with transparency set to 0.5. After PYMOL2.3, cartoon-transparency is
> supposed to work on the atom level, but when I try to apply cartoon
> transparency to the two helices as a selection
> (cartoon_transparency,0.5,sele), the helices change color but do not become
> transparent. Am I doing something wrong?
>
> --
> Criss Hartzell
> ___
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



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Re: [PyMOL] cartoon_transparency issue

[Markus Heller]

D'uh!!!

I need to get used to always ray before assuming anything.

Sorry for the noise!

-Original Message-
From: Justin Lecher [mailto:j.lec...@fz-juelich.de] 
Sent: Tuesday, August 26, 2014 4:24 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] cartoon_transparency issue

On 25/08/14 18:42, Markus Heller wrote:
 Hello,
 
 Attached is a crop of a figure create with the latest PyMOL under Windoze 7 
 64 bit.  When setting cartoon_transparency, I get a gray band on the 
 cartoons.  Where does this come from, and how do I get rid of it?
 
 Thanks and Cheers
 Markus
 
 Here's my code:
 
 # reset everything
 delete all
 
 # white background
 bg_color white
 
 # show valences
 set valence, 1
 
 # show valences inside rings, 0 = centered, 1 = inside set valence_mode, 1
 
 # antialias
 set antialias = 1
 
 # load the PDB files
 
 load ... example PDB
 
 # turn on grid mode and set it up
 set grid_mode, 1
 
 # hide everything
 hide everything
 
 # select protein
 select prot, polymer
 
 # color everything
 color white
 
 # show cartoon ribbon for protein
 show cartoon
 
 # don't show backbone for cartoons
 set cartoon_side_chain_helper, on
 
 # keep standard helix, strand, loop representations # other options: cartoon 
 loop, cartoon rect, # cartoon oval , cartoon tube cartoon automatic
 
 # color cartoon white and set transparency set cartoon_color, white set 
 cartoon_transparency, 0.7
 
 # select residue of interest
 select roi, resi 27+31+34+37+41
 
 # show sticks for ROIs
 show sticks, roi
 
 # hide non-polar H
 hide (h. and (e. c extend 1))
 
 # color ROIs
 color atomic
 color yellow, (name C* and roi)
 
 # show H-bonds between sidechains and assign to slots dist Hbo-sc, resi 37, 
 resi 41, mode = 2
 
 # hide alls labels
 hide labels
 
 # color all dashes green
 set dash_color, green
 
 # deselect all to avoid little pink squares deselect
 
 
 
 
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Hi markus,

just raytrace you figure using the ray command.

Justin

-- 
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117



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Re: [PyMOL] cartoon_transparency issue

[Justin Lecher]

On 25/08/14 18:42, Markus Heller wrote:
 Hello,
 
 Attached is a crop of a figure create with the latest PyMOL under Windoze 7 
 64 bit.  When setting cartoon_transparency, I get a gray band on the 
 cartoons.  Where does this come from, and how do I get rid of it?
 
 Thanks and Cheers
 Markus
 
 Here's my code:
 
 # reset everything
 delete all
 
 # white background
 bg_color white
 
 # show valences
 set valence, 1
 
 # show valences inside rings, 0 = centered, 1 = inside set valence_mode, 1
 
 # antialias
 set antialias = 1
 
 # load the PDB files
 
 load ... example PDB
 
 # turn on grid mode and set it up
 set grid_mode, 1
 
 # hide everything
 hide everything
 
 # select protein
 select prot, polymer
 
 # color everything
 color white
 
 # show cartoon ribbon for protein
 show cartoon
 
 # don't show backbone for cartoons
 set cartoon_side_chain_helper, on
 
 # keep standard helix, strand, loop representations # other options: cartoon 
 loop, cartoon rect, # cartoon oval , cartoon tube cartoon automatic
 
 # color cartoon white and set transparency set cartoon_color, white set 
 cartoon_transparency, 0.7
 
 # select residue of interest
 select roi, resi 27+31+34+37+41
 
 # show sticks for ROIs
 show sticks, roi
 
 # hide non-polar H
 hide (h. and (e. c extend 1))
 
 # color ROIs
 color atomic
 color yellow, (name C* and roi)
 
 # show H-bonds between sidechains and assign to slots dist Hbo-sc, resi 37, 
 resi 41, mode = 2
 
 # hide alls labels
 hide labels
 
 # color all dashes green
 set dash_color, green
 
 # deselect all to avoid little pink squares deselect
 
 
 
 
 --
 Slashdot TV.  
 Video for Nerds.  Stuff that matters.
 http://tv.slashdot.org/
 
 
 
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
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Hi markus,

just raytrace you figure using the ray command.

Justin

-- 
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117




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