Wikipedia:WikiProject Molecular Biology/Molecular and Cell Biology/Votes/protein rendering application

This vote closed on the 7th of December - Pymol will be the supported tool of the MCB group for molecular image rendering. --Username132 (talk) 14:25, 11 December 2006 (UTC)

Having been under discussion for some time, I feel the topic of choosing a supported image rendering application should be ready to come to a vote. The question is, which application would likey be the quickest to learn and provide the most important features required for the most common rendering needs? This likely procludes the applications with cluttered interfaces and specialist features (such programs would not be restricted in their use; we simply wouldn't direct newbies towards these more complicated applications). After the vote closes, I hope that a tutorial will be written detailing how to get the protein sequence and what to do with it with regards to the chosen program.

--Username132 (talk) 04:02, 23 November 2006 (UTC)

Blender

[[1]]

Chimera

[[2]]

Cn3D

[[3]]

Molmol

[[4]]

Molscript

[[5]]

Pymol

[[6]] Support - PyMol is a very flexible program with many advantages: publication quality images, support for both protein and nuclear acid representations, built-in renderer - no external program needed, an extensive wiki for help available, powerful scripting, open source, ... to name a few. --Splette :) ^{How's my driving?} 05:54, 23 November 2006 (UTC)

• Support this would be pretty unequivocal support if not for the fact that AFAIK future versions will only be released as source code, and I'm not sure I'm up to helping newbies through compiling things under Windows. Opabinia regalis 07:29, 24 November 2006 (UTC)

QuteMol

[[7]] This appears to be the only new-user-friendly one, judging by comments in the discussion, even if it is less powerful (if it has the basics, I think that's all a newbie needs). --Username132 (talk) 04:02, 23 November 2006 (UTC)

This doesn't run on my computer. TimVickers 04:15, 23 November 2006 (UTC)

I think the discussion on this one was somewhat incomplete/unorganized because it was added later. It's a nice little program, but it's very new and has a lot of development left before it'll be ready for general use. Although its shader is outstanding, it lacks a large number of what we'd probably consider necessary features - cartoon/ribbon representations, secondary structure color schemes (or any sort of user-defined color scheme), and it's rather unstable. Opabinia regalis 07:31, 24 November 2006 (UTC)

SPDBV

[[8]]

VMD

[[9]]

YASARA

[[10]] Support - YASARA is a very flexible program full of benefits: molecular graphics, molecular dynamics, homology modelling, dedicated and universal force fields, publication quality images, support for both protein and nuclear acid representations, real-time rendering, python support for user-generated features, script/macro support, open source, automated updates & feature support. rdoherty 17:17, 5 December 2006 (UTC)

Comments

Sorry all, I started this discussion and then I disappeared. Anyhow I'd like to take the chance to explain my ideas a bit.
1. Good images remain regardless of the program they were done with
I started this discussion not to push a certain program but rather to get some amount of continuity and quality for protein representations. Of course we won't delete any existing good images (but crappy ones yes) once this vote is over just because they weren't made with the program we decided upon.
2. A recommendation, not a strict rule
Also I think this vote should be more of a recommendation rather than a strict rule. If someone doesn't like the program we agree on because he or she can produce images of superb quality with his/her program of choice: Why not?
3. Representaion is as important as the tool
As Tim mentioned some time ago, not just the program is important but also how we represent the proteins. White background vs. black? Spacefilling vs. cartoon and what about the colors? For this it would be good to start a separate discussion because the basic forms of representation are available in any good protein rendering program.
4. Tutorial
As Username132 suggested, once we decide on the program a tutorial should be written by the people who know the program well. Many programs have scripting abilities which make it easy.
--Splette :) ^{How's my driving?} 05:41, 23 November 2006 (UTC)