User:GAThrawn22/Sandbox2/

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Standardizing protein representation pictures
I think it would be nice to standardize the rendered images of proteins in some way to give the same look and feel for this kind of articles. Of course this might not be possible in all cases as there are far too many protein articles. Also there are some that have good illustrations already which should not be removed just for the sake of standardization. However for all those pictureless protein articles where an image might be useful it would be nice to use the same representation. What do you think?

I suggest to use the open source program PyMol to render the images. It is widely used, gives nice results and had cartoon representations of both proteins and nucleic acids. For some articles I am interested in I did some images: actin, Arp2/3 complex, MreB, Profilin

If you think this would be useful, I'd volunteer to render some images on request. Just leave a message on my talk page. Any thoughts?-- Splette  Talk 12:16, 1 September 2006 (UTC)

It seems that others are also interested in what's used to make protein representation pictures. There's a discussion over on the help page about what tools everyone uses. I think it's a great idea that we standardize the rendered images. We should discuss the pro's and con's of the various imaging tools and vote on it. And then produce a tutorial to instruct new users of the program how to use it and a series of guidelines so that the images all share similar standards. GAThrawn22 22:53, 2 September 2006 (UTC)


 * I left some tool suggestions on the other talk page, but I wanted to say here that I'm not sure specific guidelines on protein images are really necessary or useful. Proteins are different enough that each image might want to illustrate different features of the structure. Maybe what we want is a suggestion for what the most "basic" protein image should look like, with the understanding that more illustrative images may replace the basic one for proteins with interesting features - which case I'd say as a first approximation: cartoon or ribbon representation colored by index or secondary structure. I'd be happy to work on a tutorial/help page if the "recommended" program or programs is one that I'm familiar with. Opabinia regalis 00:13, 3 September 2006 (UTC)


 * I think Opabina might be right in that when it comes to highlighting specific features, another program might be more suitable (I've never operated any of these programs). The recommended program (for which a tutorial page would be ideal) should be relatively quick and easy to use and produce good output. So... what are the pros and cons (fill in the thing at the bottom of this discussion with any points that spring to mind)? Username132 (talk) 11:10, 4 September 2006 (UTC)

{|width="100%" way to give the same look and feel for this kind of articles. Of course this might not be possible in all cases as there are far too many protein articles. Also there are some that have good illustrations already which should not be removed just for the sake of standardization. However for all those pictureless protein articles where an image might be useful it would be nice to use the same representation. What do you think?
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I suggest to use the open source program PyMol to render the images. It is widely used, gives nice results and had cartoon representations of both proteins and nucleic acids. For some articles I am interested in I did some images: actin, Arp2/3 complex, MreB, Profilin, Zinc finger(Protein + DNA)

If you think this would be useful, I'd volunteer to render some images on request. Just leave a message on my talk page. Any thoughts?-- Splette  Talk 12:16, 1 September 2006 (UTC)

It seems that others are also interested in what's used to make protein representation pictures. There's a discussion over on the help page about what tools everyone uses. I think it's a great idea that we standardize the rendered images. We should discuss the pro's and con's of the various imaging tools and vote on it. And then produce a tutorial to instruct new users of the program how to use it and a series of guidelines so that the images all share similar standards. GAThrawn22 22:53, 2 September 2006 (UTC)


 * I left some tool suggestions on the other talk page, but I wanted to say here that I'm not sure specific guidelines on protein images are really necessary or useful. Proteins are different enough that each image might want to illustrate different features of the structure. Maybe what we want is a suggestion for what the most "basic" protein image should look like, with the understanding that more illustrative images may replace the basic one for proteins with interesting features - which case I'd say as a first approximation: cartoon or ribbon representation colored by index or secondary structure. I'd be happy to work on a tutorial/help page if the "recommended" program or programs is one that I'm familiar with. Opabinia regalis 00:13, 3 September 2006 (UTC)


 * I think Opabina might be right in that when it comes to highlighting specific features, another program might be more suitable (I've never operated any of these programs). The recommended program (for which a tutorial page would be ideal) should be relatively quick and easy to use and produce good output. So... what are the pros and cons (fill in the thing at the bottom of this discussion with any points that spring to mind)? Username132 (talk) 11:10, 4 September 2006 (UTC)


 * Nice to get so much feedback. Seems like there is quite some interest in the topic here. I think the list below so far summarizes the pros and cons of the different programs quite well. However I guess we are not in a rush to make a decision, so should we wait a bit more before starting to vote? -- Splette [[Image:Happyjoe.jpg]] Talk 09:02, 7 September 2006 (UTC)


 * Yeah, I think so. There aren't enough people commenting and some of the programs pros and cons are still blank (thanks for the work you put into that, Opabinia) - The next news letter should inform the readers of the change of discussion layout and urge people to get involved in the discussion of proposals particularly. --Username132 (talk) 18:12, 7 September 2006 (UTC)

Pymol

 * Pymol

Pros

 * Commonly used for visualization
 * Integrated internal raytracer - produces very nicely shaded images without an external raytracer such as POV-Ray
 * Basic manipulations are fairly straightforward for new users
 * Especially nice cartoon/secondary structure manipulation
 * Very easy scripting, either in internal commands or in Python
 * Free and open-source
 * Advanced users can make excellent movies surprisingly easily

Cons

 * Documentation significantly lags behind new releases
 * Beyond the basic features, not especially user-friendly
 * Idiosyncratic selection syntax
 * Looks like in the long term, the "free" version will be only distributed as source code, while only paid subscribers will have access to compiled versions
 * Poor selection of tools for trajectory analysis inhibits the usefulness of those movies
 * Electrostatic calculations are unstable and "under development"
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Molmol

 * Molmol

Pros

 * Publication-quality images
 * For example, see Pi helix, Ferredoxin fold, Beta-propeller domain
 * Freely available here and open-source (not GPL, though)
 * Easy to use and learn; online tutorial available
 * Excellent selection language and control of ribbon, bond, atom, etc. parameters such as size and color
 * Built-in calculators for many features (2ndary structure, dihedral angles, electrostatic potentials, etc.)
 * Excellent for NMR structures, e.g., sausage diagrams
 * Simple to extend with macros
 * Decent set of output image formats
 * Decent documentation built into program itself

Cons

 * No longer under development?
 * Trajectory animation is relatively primitive
 * Annoyingly hard to do a few simple tasks, e.g., label side chains and make rainbow ribbon diagram
 * Depiction of electrostatic/electron density surfaces hard to learn; Chimera is much better


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VMD

 * VMD

Pros

 * Extremely common (at least in the molecular dynamics and structure prediction communities) and well-established
 * Most basic manipulations are fairly easily accessible to new users
 * Good documentation
 * Easy to produce standardized images; could distribute a script specifying our desired standard parameters
 * Compiled versions for most OSes; source code also available
 * Many options for image export, including POV-Ray and Tachyon files for raytracing

Cons

 * Licensing is free but does require registration
 * Many integrated tools may be overkill for our purposes
 * Without significant customization, VMD images are often recognizable as VMD images (like Excel plots are recognizable as Excel plots)
 * Can be clunky to export a basic, non-raytraced image


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Chimera

 * Chimera

Pros

 * High-quality images
 * A good balance of user-friendliness and flexibility
 * Good documentation
 * License does not require academic affiliation
 * Downloadable binaries for most OSes
 * Lots of cool tools, especially the sequence viewer and volume/surface represenations

Cons

 * Newer and less widely used than other alternatives
 * "Feature creep"; some features/options aren't likely to be used and just clutter the work surface
 * Interactive tools work slightly differently than other programs (VMD in particular); can be difficult to switch
 * No source code
 * Stability issues under Linux with certain X configurations
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Mol Script

 * MolScript

Pros

 * Publication-quality images
 * We could plausibly distribute a standard script so that users only need to change the target PDB file
 * Probably the most powerful/flexible option in terms of illustrating specific features

Cons

 * Clunky licensing requirements (must have, or have had, some academic affiliation)
 * Distributed as source code; can be fussy to compile and install
 * Heavy on command-style scripting
 * User-unfriendly, especially to those with no Linux experience


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SwissPDBviewer

 * SPDBV

Pros

 * Often recommended to students - if someone has used only one program, it's probably either this or Rasmol

Cons

 * Not as powerful as other options; fewer analysis tools


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