[PyMOL] Transparency in cartoons
Hello! I'm trying to show some aminoacids transparent in a cartoon view. I use the command cmd.set(transparency, 0.8 ,(resi + values[0] + : + values[1] + )). When i see the cartoon view, happens nothing, but if I use show surface the transparency is shown. Do you know how to do it in the cartoon view? Thanks! Toni
Re: [PyMOL] Transparency in cartoons
On Tuesday 22 January 2008 10:10:58 Toni Pizà wrote: I'm trying to show some aminoacids transparent in a cartoon view. I use the command cmd.set(transparency, 0.8 ,(resi + values[0] + : + values[1] + )). When i see the cartoon view, happens nothing, but if I use show surface the transparency is shown. Do you know how to do it in the cartoon view? There is a separate setting cartoon_transparency. The Edit all... option in the Setting menu provides an overview of all available parameters. There are also predefined transparency settings available in the Display menu. Cheers, -- Lieven Buts Ultrastructure Laboratory Vrije Universiteit Brussel
Re: [PyMOL] Distance and scripts
On Monday 21 January 2008 23:51:15 Toni Pizà wrote: I'm not sure this is what you're asking, but I use scripts by typing: @script.pml Thanks for your response, but I'm asking how to pass arguments to pymol's scripts written in Python. I type run nameOfScript.py within pymol for this, but I would pass some arguments, such as run script.py arg0 arg1. The convential solution is to run a script that uses the extend command (see help extend) to add a Python function as a new PyMOL command. This command can take any arguments you define for the function. Cheers, -- Lieven Buts Ultrastructure Laboratory Vrije Universiteit Brussel
[PyMOL] Subject: Transparency in cartoons
When i see the cartoon view, happens nothing, but if I use show surface the transparency is shown. Do you know how to do it in the cartoon view? Toni, Set the cartoon_transparency, not just transparency. Here's the appropriate PyMOLWiki link: http://www.pymolwiki.org/index.php/Cartoon_transparency -- Jason -- Jason Vertrees (javer...@utmb.edu) Doctoral Candidate Biophysical, Structural Computational Biology Program University of Texas Medical Branch Galveston, Texas http://www.best.utmb.edu/ http://www.pymolwiki.org/
Re: [PyMOL] PyMOL-users Digest, Vol 20, Issue 6
Hi Toni, I think the variable you want to set is cartoon_transparency not transparency. The way I figured this out was through the menu-settings-Edit All... dialog box. Matt Date: Tue, 22 Jan 2008 10:10:58 +0100 From: Toni Piz? servo...@gmail.com Subject: [PyMOL] Transparency in cartoons To: pymol-users@lists.sourceforge.net Message-ID: b3909a070801220110w435779f9l5917e1a0c78e5...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hello! I'm trying to show some aminoacids transparent in a cartoon view. I use the command cmd.set(transparency, 0.8 ,(resi + values[0] + : + values[1] + )). When i see the cartoon view, happens nothing, but if I use show surface the transparency is shown. Do you know how to do it in the cartoon view? Thanks! Toni -- - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
