Re: [PyMOL] Transparent Background in Educational Version

[Emilio Xavier Esposito]

Hi Cris
Please include the ray=1 option in your png test.png, dpi=300 command or
use the set opaque_background, off instead of the set
ray_opaque_background, off command.

Commands to create a PNG file with a transparent background:

set opaque_background, off

png test.png, dpi=300, ray=1

*PNG file creation*
https://pymolwiki.org/index.php/Png

*Opaque background*

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

Emilio
​

On Fri, Jan 27, 2017 at 12:27 PM, cristopher garduno  wrote:

> Hello, my name is Cris and I am attempting to save a version of my protein
> with a transparent background. I have tried using the commands
>
>
> set ray_opaque_background, off
>
> png test.png, dpi=300
>
>
> but this doesn't seem to work. I have the educational version of PyMol, is
> this the reason that I'm unable to use the option for a transparent
> background?
>
> Thank you,
> Cris
>
> --
> Cristopher D. Garduno Luna
> Neuroscience, B.S.
> Class of 2017
> University of California, Los Angeles
> garduno.c...@gmail.com
> Curriculum Vitae 
>
> 
> --
> Check out the vibrant tech community on one of the world's most
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Re: [PyMOL] Connectivity

[Thomas Holder]

Hi Laurie,

The list of bonds is accessible with cmd.get_model(), see
https://pymolwiki.org/index.php/Get_Model

PyMOL> m = cmd.get_model()
PyMOL> print m.bond[0].index
[0, 1]
PyMOL> print m.bond[0].order
1

Cheers,
  Thomas

On 26 Jan 2017, at 13:50, Laurence Williams  wrote:

> Dear pymol users,
> 
> I understand that pymol does not explicitly need connectivity data to 
> visualise molecules as bonds are drawn when two atoms are within in a given 
> distance. However, once those bonds are drawn for the molecule, is 
> connectivity data stored somewhere whilst the file is in use? I ask with the 
> aim to extract that data into a python object.
> 
> Thanks
> Laurie

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] Transparent Background in Educational Version

[cristopher garduno]

Hello, my name is Cris and I am attempting to save a version of my protein
with a transparent background. I have tried using the commands


set ray_opaque_background, off

png test.png, dpi=300


but this doesn't seem to work. I have the educational version of PyMol, is
this the reason that I'm unable to use the option for a transparent
background?

Thank you,
Cris

-- 
Cristopher D. Garduno Luna
Neuroscience, B.S.
Class of 2017
University of California, Los Angeles
garduno.c...@gmail.com
Curriculum Vitae 
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net