Thursday, January 20, 2011 2:36 PM
> To: 'pymol-users@lists.sourceforge.net'
> Subject: [PyMOL] colors and font size while ray tracing
>
> Hello:
> I am trying to generate stereo figures for my manuscript. When I try
to
> ray trace at higher resolution, the font size (I us
Hello:
I am trying to generate stereo figures for my manuscript. When I try to ray
trace at higher resolution, the font size (I use label_font_id=4) is becoming
very small. If I use any fonts from the settings tab, the font size doesn't
change with ray tracing. If I am correct, many journals pre
Hi all;
I am currently writing a little script that takes a selection and creates a
hydrophobicity plot (using matplotlib). For the plot it would be nice to have
the color of the used residues and I partially succeed
with the iterate-color construct:
cmd.iterate(sele-str, "stored.list.append(c
But does this problem look like a bug ?
No, it works as intended. The issue here is that the GUI just does not (yet)
provide the capability of coloring representations, just atoms. So if you
color representations directly using a command, then you'll need to use a
command uncolor them.
At
-Original Message-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Sebastien Moretti
> Sent: Monday, October 17, 2005 11:45 PM
> To: pymol-users
> Subject: [Re: [PyMOL] [colors frozen for rendering modes
&g
Sebastien,
I cannot
change the color for rendering modes I defined.
I do not understand what you mean by this.
Cheers,
Warren
I mean that the color, for cartoon view, is unchangeable when 'set
cartoon_color' is defined in the $HOME/.pymolrc file.
Thus, when I define 'set cartoon_color' in
Sebastien,
* Sebastien Moretti [2005-10-17 08:41]
wrote:
> >Sebastien,
> >
> >>I cannot
> >>change the color for rendering modes I defined.
> >
> >I do not understand what you mean by this.
> >
> >Cheers,
> >Warren
>
> I mean that the color, for cartoon view, is unchangeable when 'set
> carto
Sebastien,
I cannot
change the color for rendering modes I defined.
I do not understand what you mean by this.
Cheers,
Warren
I mean that the color, for cartoon view, is unchangeable when 'set
cartoon_color' is defined in the $HOME/.pymolrc file.
Thus, when I define 'set cartoon_color' in
Hello,
I defined some default colors in the $HOME/.pymolrc file.
E.g.: set cartoon_color, slate
It works fine but in PyMOL viewer (version 0.98) I cannot change the
color for rendering modes I defined.
The one I defined is always kept.
Is this a normal behavior ?
Thanks
--
Sébastien Morett
2005 9:00 AM
> To: pymol-users@lists.sourceforge.net; ccp...@dl.ac.uk
> Subject: [PyMOL] Pymol colors and selections
>
> I'm having PYMOL trouble with something that should be easy:
>
> I want to make a green ribbon diagram, a grey transparent
> surface, and then display residue s
I'm having PYMOL trouble with something that should be easy:
I want to make a green ribbon diagram, a grey transparent surface, and
then display residue side chains in red underneath. I'm having trouble
with selections that set up these three items as discrete things I can
color as I choose.
> I just discovered that I can't set colors with more than one
> decimal point
> of precision. Is there any way around this? I'm trying to get a
> background that blends in with part of a web page.
>
Not true... just the output is rounded. The exact color is whatever you set it
to.
PyMOL>se
I just discovered that I can't set colors with more than one decimal point
of precision. Is there any way around this? I'm trying to get a
background that blends in with part of a web page.
Nathaniel Echols
cs Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 FAX:(650)-266-3501
> -Original Message-
> From: Peter Stogios [mailto:pstog...@uhnres.utoronto.ca]
> Sent: Tuesday, May 28, 2002 9:08 AM
> To: pymol-users@lists.sourceforge
This topic was touched on before but I'm still having problems with it.
Somebody asked how to color sticks differently from cartoons and Warren
explained that this can be done by creating duplicate objects. I managed
to accomplish that, but when I ray-trace the image the cartoon takes the
same co
Mario,
> From: Mario Sanchez [mailto:sanc...@if.sc.usp.br]
> I have some questions using pymol and I wonder if someone can give me
> some help.
>
> At first I would like to know if there are any way to define
> more colors
> than that appearing in the menu. Is there some kind of "rgb"
> definit
I have some questions using pymol and I wonder if someone can give me
some help.
At first I would like to know if there are any way to define more colors
than that appearing in the menu. Is there some kind of "rgb" definition,
for exemple?
I also tried to change the colors of the sticks only, with
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