My software notes

April 6, 2007

[PyMOL] black-white cartoon view

Filed under: pymol/ molmol — kpwu @ 5:59 pm

I still remember 10 years ago when I was learning what is a protein, what’s the structural elements of a protein. I always saw protein structure which was presented as black-white mode, or gray gradient mode. Today, I found that PyMOL has a command to generate structure figures like the old fashion.

Here is the example :
1. I load 2GB1 and make a regular cartoon view
regular ray
2. I change the background color to white (bg_color white) and change the ray_mode by type “set ray_trace_mode, 2“. That will change the trace mode to make a black-white mode for rendering. At this moment, your pymol viewer still shows you the colorful structure, that’s okay and don’t worry. Then use “ray“, you will generate a black-white cartoon and see the result immediately.

3. To be very real “old fashion”, change the helix representation to cylindrical mode “cartoon_cylindrical_helices, 1” to activate the cylindrical helices mode “on”. I rotate the structure to make it easier to see the effect of cylindrical helix in 2GB1.
black-white ray

4. If you don’t like the thick black line, that’s okay. Just type “set antialias, 2” to make the black line thiner. Then do the same thing, use “ray” to generate a black-white structure. Here is the final result:

5. One more, but not the last (if I got some ideas, I will keep post more examples). I change the background color to cyan  “bg_color cyan“. And do the black-white picture generation. The result is fantastic. It’s easier than using some photo editors to make such graph. Here is the result:
2gb1 nice bkg


Protein NMR Spectroscopy: Principles and Practice

Filed under: book_list — kpwu @ 4:34 pm

protein nmr spectroscopyHonestly, this book is really a “bible” for people doing NMR. I learned most of my NMR knowledge by reading this book in 2001. I still remember that moment that KM and I spent every Wednesday night to discuss the content of each chapter.

The one I had read was first edition which was published in 1996. In Jan. 2007, I finally got the second edition from amazon after the pre-ordered I made in Aug. 2006. The new edition adds lots of new NMR techs e.g. RDC, TROSY, slow motion dynamics and so on.

In summary, this is really a good book and a NMR person should keep it in hand as a tool book and a reference book. Dr. Palmer also constructs a website to provide the update, errata and other information about this book. The URL is here:

Author: John Cavanagh, Wayne J. Fairbrother, Arthur G. Palmer, III, Nicholas J. Skelton, Mark Rance
Format: Hardcover, 854 pages
Publication Date: November 2006
Publisher: Academic Press
Dimensions:9.25″H x 6.25″W x 1.75″D; 2.84 lbs.
ISBN-10: 012164491X
ISBN-13: 9780121644918
List Price: $86.95

Elsevier/Academic press
amazon link

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