Tag Archives: publication

Jane – Journal/Author Name Estimator

Jane – Journal/Author Name Estimator is a new web based application that can suggest potential reviewers or target journals for a manuscript based on its title and abstract. It was just published by Bioinformatics under Advance Access (but unfortunately it’s not an open access article). I have tested two of my upcoming publications and Jane performed well: I wasn’t surprised by most of predicted names and journal titles. The topic I’m writing about in these papers is rather narrow, so don’t treat it as any performance measure – test it yourself, if you are interested.

Probably I’m not going to use it as authors suggested – I consider this application a helpful literature research tool.

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Posted by on January 28, 2008 in bioinformatics, Papers, Research, Services


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Protein cartoons with Pymol

Here is a short tutorial on the protein cartoons with Pymol. I picked as an example a hemoglobin and focused only on the cartoon representation of the protein, but keep in mind it does not necessarily explores all options of this software. Also, since I’m blind to stereo images, I’m not sure if all of following tips make sense with stereo representation of molecules.

  1. Change protein representation to cartoons.
  2. Turn off depth cue (under”Display”) – unless you want to put an accent on some part of the protein this option is unnecessary, because it’s hard to get 3D feeling from a 5cm on 5cm print.
  3. Turn off specular reflections (under “Display”) – most likely printer is able to show less colors than your screen, and will render specular reflections as harsh white blobs
  4. Change background color into white (as above) – that’s obvious, black background is for viewing on screen
  5. Change view to orthoscopic (as above) – maybe it’s a matter of a personal taste, but perspective view (default in Pymol) creates unnecessary distortions, that again do not help in shape perception on the small print
  6. Turn on option of “fancy helices” (“Settings/Cartoons”) – this renders helices with tubular edges like in Molscript (leave it off if you don’t like it)
  7. Turn on option “smooth loops” (as above) – perception of the secondary structure elements arrangement becomes much easier
  8. Turn on option “highlight color” (as above) – again, it’s a matter of a personal taste; this option make an internal surface of helices grey (you may change the color via command line)
  9. Turn shadows off (“Settings/Rendering/Shadows”) – I feel that on a small print they only disturb the image

What I also do is turning on matte finish on the cartoons. While it doesn’t necessarily look better on the screen, when in print it helps to mask printing artefacts (like raster), when looked at from normal viewing distance.

Then you can test these settings by clicking “Ray”. If you like the final image, save it, read its dimensions and multiply them by 3. Then type into command-line box: ray multipliedX, multipliedY and press enter.

Below I embedded a video showing more or less what I’ve just described.

Feel free to comment if you have any suggestions on improving this process.


Posted by on December 12, 2007 in Software, Visualization


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