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Growth might be the lifeblood of a business, but it isn't always the best or most sustainable way to create value for shareholders. Return on invested capital (ROIC) is often just as important—and occasionally even more so—as a measure of value creation and can be easier to sustain at a high level.
When a company's ROIC is already high, growth typically generates additional value. But if a company's ROIC is low, executives can create more value by boosting ROIC than by pursuing growth (Exhibit 1). A close look at companies with high price-to-earnings multiples shows that many have extraordinary returns on capital but limited growth. This scrutiny suggests that, contrary to conventional wisdom, investors recognize (and will pay more for) the anticipated returns of companies with a strong ROIC, despite their limited growth prospects. This observation doesn't mean that growth is undesirable; unless companies keep up with their industries, they will likely destroy value. But they shouldn't pursue growth heroically at the expense of improvements in ROIC.
After identifying the largest publicly listed companies in the United States (by revenues) in 1965, 1975, 1985, and 1995, we examined their long-term patterns of growth and ROIC.1 1.
The performance of each set of companies was tracked as a portfolio until 2004. The median ROIC for the 1965 group remained stable, at about 9 percent, over the next 40 years. We observed the same pattern for the groups from 1975, 1985, and 1995. In other words, ROIC tends to remain stable over time (Exhibit 2).
Growth, by contrast, is fleeting. The median inflation-adjusted growth in revenues for the top 500 companies in 1965 started out at 7 percent and steadily declined to 2 percent over the next 10 years, hitting a cyclical low of 0 percent by year 17. For the next 20 years, growth hovered at around 2 percent—a figure below the level of US GDP growth.2 2.
Real GDP growth averaged around 2.5 to 3.5 percent a year from 1929 to 2005. We observed a similar general pattern of decay in median real growth for the top 500 companies in 1975, 1985, and 1995.
Moreover, pattern analysis at the industry3 3.
Defined by the Global Industry Classification Standard (GICS). level further shows the importance of managing ROIC. A comparison of ROIC4 4.
Measured by the median ROIC of companies that survived in subsequent years. for the top 500 companies of 1965 shows that it remained steady in most sectors and even increased in some—particularly those with strong brands or patent-protected products (household and personal goods, for example) and pharmaceuticals and biotechnology (Exhibit 3, part 1). Growth, by contrast, almost always declined, except in pharmaceuticals (Exhibit 3, part 2).
A close look at individual companies finds similar patterns; companies with high levels of ROIC tend to hold on to that advantage, whereas high-growth companies rarely do. Exhibit 4 looks at the probability that a company will migrate from one level of ROIC to another over the course of a decade. A company that generated an ROIC of less than 5 percent in 1994, for instance, had a 43 percent chance of earning less than 5 percent in 2003. As the exhibit shows, low and high performers alike demonstrate consistency throughout the 40-year period. Companies with an ROIC of 5 to 10 percent had a 40 percent probability of remaining in the same group ten years later; companies with an ROIC of more than 20 percent had a 50 percent probability.
But when it comes to growth, companies are very likely to experience substantial declines (Exhibit 5). Of companies that grew by more than 20 percent in 1994, for example, 56 percent were growing at real rates of less than 5 percent ten years later. Only 13 percent of the high-growth companies maintained 20 percent real growth ten years on, and acquisitions probably drove most of it.
Bing Cao and Bin Jiang are consultants and Tim Koller is a partner in McKinsey's New York office.
This article was first published in the Spring 2006 issue of McKinsey on Finance. Visit McKinsey's corporate finance site to view the full issue.
February 2006—Finance theory isn't enough when companies set their expectations for reasonable returns on invested capital. A long-term analysis of market and industry trends can help.more
October 2005—Return on capital is the benchmark for comparing performance between businesses. But new math is needed when a company's capital intensity is low.more
October 2005—TRS doesn't reflect a company's performance or health. What does?
August 2005—The largest corporations rarely sustain strong growth unless they compete in the right places at the right times.more
March 2005—Earnings per share and share prices aren't the whole story—particularly in the medium and long term.more
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A brilliant film. Would it have been even more powerful as an experiment (ie real) rather than acted? Read More
About SixtySecondView
Sixtysecondview is a series of occasional one minute viewpoints. Initially they were all video interviews with figures from business, media, government and NGOs on topics of the moment with a public relations or public affairs flavour.
But this proved too restrictive so I use the keyboard now too, but I do try and keep them short so that it will take the average reader no longer than a minute to get through.
Tagsadvertising All Blacks AME APACMEA Asia Pacific Australia Beijing Burson-Marsteller Business Campaign China content Cultural Connections design Design Royale Digital Edelman Edelman Melbourne events experiential Facebook Geek Government Grant Smith H&K harris India Indonesia Insights Japan Malaysia media Michelle Hutton Middle East New Zealand NGOs PR Public Relations Rugby Singapore trust Trust Barometer UAE Vietnam Words of a Generation

subset: commoncrawl


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Suge Knight's ex fiancée, Stormey Ramdhan, speaks on her life with the former CEO of Death Row Records and why she's spilling secrets in her new tell-all book. Stromey talks about Suge's relationship with their two sons and about her 20-year love affair with Suge.
Get an excerpt of the February 2014 Q&A with Stormey below.
Jamie: What kind of relationship does [your son] have with Suge?
Stormey: That's unfortunately the saddest part of the book: The relationship dissipated when Suge decided that he didn't want to be a part of our lives anymore. I think he made a decision not to be a part of many people's lives that loved him. But ours in particular he did an about-face and walked away from my children and the responsibility of taking care of the children and being involved in their lives. He was once there for football games, and then all of a sudden whatever he was going through was more important than being a dad. So that part affected my kids, and they had to figure it out on their own and realize that they weren't going to have that support from their father.
There's more to Stormey's story. Get it in the February 2014 issue of Sister 2 Sister.


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UN.GIFT Publications
IOM Manual on THB crimes typologies. Russian.
Jan 14 2011
Download right click "save as"
The Manual illustrates mechanisms of human trafficking crimes, on the basis of a typological classification while providing methodological recommendations on effective investigative approaches. The manual focuses on judicial practice, criminal characteristics of human trafficking and typology of victims of trafficking. The manual has been published in 1000 copies and was developed in close cooperation with the United Nations Office on Drugs and Crime (UNODC). The authors are specialists of the Moscow University of MoI Russia, Prosecutor's General Academy and the Russian Academy of Advocacy and Notariate. For more information visit the website of IOM.
Trafficking in childrenChange TagAll Publications
- 2014 Global Trafficking in Persons report - full
- US State Department Trafficking in Persons Report 2014
- 3rd General report on GRETA's activities
- Walk Free Global Slavery Index 2013
- UNESCO: Model curricula for journalism education: a compendium of new syllabi
- ILO: Marking progress against child labour: Global estimates and trends 2000-2012
- IOM: A Situational Analysis of Aruba's Response to Human Trafficking
- Current Status of Victim Service Providers and Criminal Justice Actors in India on Anti-human Trafficking
- OSCE: Trafficking in Human Beings Amounting to Torture and other Forms of Ill-treatment
- Report of the Special Rapporteur on trafficking in persons, especially women and children, Joy Ngozi Ezeilo
- Policy and legislative recommendations towards the effective implementation of the non-punishment provision with regard to victims of trafficking
- European Commission The statistical report on trafficking in human beings 2013


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Product Information:
Product Details
Weights & Dimensions
|Material: Plastic
|Food Creation: Cakes; Cookies; Cupcakes
|Storage Case: No
|Oven Safe: No
|Microwave Safe: No
|Dishwasher Safe: No
|Refrigerator Safe: Yes
|Color: Yellow
|Non Toxic: Yes
|Odor Resistant: Yes
|Non-Stick Surface: No
|Product Type: Cookie Cutters
|Freezer Safe: Yes
|Handles: No
|Recipes Included: No
|Commercial Use: Yes
|Country of Manufacture: Italy
|Assembly Required: No
|Additional Parts Required: No
|Product Warranty: 1 Year warranty
|PTFE or PFOA Free: Yes
About the ManufacturerWorld Cuisine sends you world class cookware, bakeware, cutlery, and appliances from around the globe. With its diverse selection, it is no wonder that people choose World Cuisine above everyone else. World Cuisine cookware embodies poise and style, while its bakeware helps combine tradition with modernity. Choose from quality World Cuisine frying pans and skillets, dutch ovens, sauce pans, grill pans, fondue sets, cookware utensils, bakeware, mixing bowls, pastry bags and more!
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Valentine's Day is here before you know it, so if chocolate is something you crave, why not make it healthier with these petite loaves made with love... by you!
Whole wheat mini banana bread made with ripe bananas and chocolate chips are sure to leave a smile on anyone's face.
These make 8 large muffins in comparison to using a normal sized muffin tin which gives you 12-13. If you don't have these Petite Loaf Pans you can use one large 8 x 5-inch loaf instead, cooking time will be closer to 50-60 minutes or use a regular sized muffin tin, baking them for about 25 minutes.
Because they are so large the nutritional info is a little higher, so I have also provided the nutritional info for regular sized muffins. Perhaps these cute silicone heart shaped muffin tins?
If you prefer nuts to chocolate in your banana bread see my banana nut bread recipe, hope you enjoy!!
Petite Chocolate Chip Banana Bread Loaves
Servings: 8 • Serving Size: 1 mini loaf • Old WW Points: 4 • Points+: 6 pts
Calories: 197.8 • Fat: 5.0 g • Carb: 40.8 g • Fiber: 4.0 g • Protein: 4.2 g • Sugar: 21.9 g
Sodium: 222 mg
As muffins:
Servings: 12 • Serving Size: 1 muffin • Old WW Points: 3 • Points+: 4 pts
Calories: 131.9 • Fat: 3.3 g • Carb: 27.2 g • Fiber: 2.7 g • Protein: 2.8 g • Sugar: 14.6 g
Sodium: 148.6 mg
- 3 ripe medium bananas
- 1/3 cup unsweetened apple sauce
- 1 1/4 cups white whole wheat flour
- 3/4 tsp baking soda
- 1/4 tsp salt
- 2 tbsp butter, softened
- 1/3 cup brown sugar
- 2 large egg whites
- 1/2 tsp vanilla extract
- 1 1/2 oz mini chocolate chips
- Smart Balance baking spray
Preheat oven to 325°. Spray a non-stick loaf pan with cooking spray.
Mash bananas in a bowl, set aside. In a medium bowl, combine flour, baking soda and salt with a wire whisk. Set aside.
In a large bowl cream butter and sugar with an electric mixer. Add egg whites, bananas, apple sauce, vanilla; beat at medium speed until thick. Scrape down sides of the bowl.
Add flour mixture, then blend at low speed until combined. Fold in chocolate chips. Do not over mix.
Pour batter into muffin pan; bake on the center rack for about 40 minutes, or until a toothpick inserted in the center comes out clean.


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Seemed like most of what I wore throughout my stay, was really sporty chic… made it
easy and comfortable for me!
this Joie jacket was the perfect pop of color to anything I would throw on.. can't wait for fall to arrive
to get more use out of it in LA.
ps. what looks did you most enjoy seeing throughout nyfw? sporty? quirky? boho? sophisticated? etc.
Tell me!
gotta run, have a call time at 11am right now.


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Unfortunately, Boston's management has not seen the wisdom of having a salaried sixth man, so you're not getting picked up in the draft just yet. Until they come to their senses, you can still prove your dedication by sporting the Celtics Draft Pick adjustable hat from adidas. This hat features a 3D embroidered Celtics logo over a sublimated logo fading into the background on the crown. Once management sees how much team pride you have when you're wearing this cap, they'll have to rethink their policy.
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OpenCongress allows anyone to follow legislation in Congress, from bill introduction to floor vote. Learn more about issues you care about and connect with others who share similar views.
OpenCongress was founded by the Participatory Politics Foundation in 2007 and operated as a joint project with the Sunlight Foundation until May 2013.
OpenCongress' data was updated about 8 hours ago.
Founded in 2006, the Sunlight Foundation is a nonpartisan nonprofit that advocates for open government globally and uses technology to make government more accountable to all. Visit SunlightFoundation.com to learn more.


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Relevance ranks synonyms and suggests the best matches based on how closely a synonym's sense matches the sense you selected.
Complexity sorts synonyms based on their difficulty. Adjust it higher to choose from words that are more complex.
Length ranks your synonyms based on character count.
- lists
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Common words appear frequently in written and spoken language across many genres from radio to academic journals.
Informal words should be reserved for casual, colloquial communication.
verb be affiliated with
Synonyms for is included in
verb be affiliated with
- be associated with star
- be classified among star
- be contained in star
- be included in star
- be one of star
More words related to is included in
Roget's 21st Century Thesaurus, Third Edition Copyright © 2013 by the Philip Lief Group.Cite This Source


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The Baker County Farmers Market kicked off its 2012 season under sunny skies and brisk winds at Macclenny City Park on March 3, offering something for just about everybody, including fresh vegetables, flowering and fruit-bearing plants, handmade jewelry and homemade baked goods.
For entertainment during the five-hour event from 8 am until 1 pm, there was music by the Bluegrass Breeze and clogging demonstrations by a local 4-H group.
If the first Saturday was any indication the weekly market should be a big hit this year, said Darryl Register, co-chair of the event and director of the Baker County Chamber of Commerce.
"I was very satisfied and happy," Mr. Register said. "We'd love to have more vendors. But we had seven, and during the fall run we never had more than four."


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Elizabeth and James brings a couture sensibility to the contemporary customer. Seeking to narrow the gap between designer and contemporary clothing, Ashley and Mary-Kate Olsen act as muses and co-designers on this new fashion label. Inspired by the mix of uptown and downtown, masculine and feminine, and casual and dressy, look to Elizabeth and James for fashion forward styles made effortless.
If an item you would like to purchase is out of stock, you can place a Special Order Inquiry. REVOLVE will then check the availability and obtain an approximate arrival date for the item, if available. Typically, it takes up to 3-4 weeks to verify this information.
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Founded in 1989, BCBGMAXAZRIA is the vision of one man: founder, designer, chairman and CEO Max Azria. Named for the French phrase bon chic, bon genre, a Parisian slang meaning good style, good attitude, the brand embodies a true combination of European sophistication and American spirit. The collection is a resulting line of directional, sophisticated designs in the most luxurious fabrics. Celebrities such as Angelina Jolie, Sarah Michelle Gellar, Rachel Bilson and Eva Mendes amongst many others, are huge fans of the brand.
If an item you would like to purchase is out of stock, you can place a Special Order Inquiry. REVOLVE will then check the availability and obtain an approximate arrival date for the item, if available. Typically, it takes up to 3-4 weeks to verify this information.
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A foolproof method for making perfect brown rice that is never sticky.
I can make white rice in my sleep, rice was a staple in my home growing up and a task my mom taught me at an early age. So naturally you would think making brown rice would come easy to me. Nope!
I never liked making brown rice because it was hit or miss... until I found this recipe on Saveur. Now I can make perfect brown rice every time and because I make large batches, I use it during the week to create easy sides.
I've played around with the original recipe quite a bit and found the perfect ratio of rice to water. If you are making 2 or 3 cups of rice, double or triple the recipe.
A few ways to make brown rice fabulous...
Chicken Sausage Brown Rice Stuffing
Dirty Brown Rice
Stuffed Pepper Soup
and I've even used it in place of white rice for my
Fiesta Lime Rice
What's your favorite way to enjoy brown rice?
Perfect Brown Rice Every Time
Servings: 5 • Serving Size: 3/4 cup • Points +: 4 pts • Smart Points: 4
Calories: 150 • Fat: 0 g • Protein: 3 g • Carb: 32 g • Fiber: 1 g • Sugar: 0 g
- 1 cup natural brown rice (I used long grain)
- 8 cups cold water
- 1 1/2 tsp kosher salt
Rinse the rice with cold water for 30 seconds. Bring the water and salt to a boil over high heat in a large heavy pot with a tight fitting lid.
When the water is boiling add the rice, stir and partially cover (don't cover complete or it will spill over) and cook on medium-high heat for 30 minutes.
Drain the rice in strainer, then quickly return to the pot and cover tightly for 20 minutes so the steam finishes cooking the rice. Uncover the rice and fluff with a fork.
Makes about 3 1/2 cups. Different rice varieties may yield different amounts.
Adapted from Saveur


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Middleton Guardian
Place an advert in the Middleton Guardian classified ads pages for a wide variety of items and events, including private property or trade property listings, private motor or trade motor sales, family notices, items for sale, lost and found notices, local events, entertainment and leisure, home services, business to business sales and services and much, much more.
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- Bruck Lighting Bling I Down Light Pendant
Bruck Lighting Bling I Down Light Pendant
Product Description
Bling is a unique hand crafted glass with an angel hair string drip design with a traditional lamp shade shape.
- The Uni-plug design allows Bling I Down pendant to be mounted on any lighting system or ceiling canopy through the use of an appropriate adaptor, not included. Standard cable length of 59" can be field-cut or specified when ordering. May be specified with Kiss canopy by adding /MP to part number or /MP2 for 2" version
- 12V AC/DC Input
- Accommodates 50W Max 12V Halogen GY6.35 Lamp (Not included)
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The stunning glass from Bruck Lighting is hand blown in various locations across the globe, including Italy, Austria, Germany and the United States. Professional glass making, which originated during the Roman Empire, is a painstaking process where only true perfection is accepted and the rejected pieces are broken up and recycled. All of our glass artisans are highly experienced and gifted in the art of glass making. These artisans choose only the top quality glass batch to start off their process. Then, the glass is meticulously mouth blown in a series of furnaces ranging in temperature, as to create the perfect shape. Since each piece is individuality hand blown, every item is a unique and rare piece of art. No one in the world will have the same exact piece of glass. As the glass is being refined in the multi-furnace process, different colors of glass are added, making it a multi colored cornucopia of depth and hue. Finally, fine craftsman tools are used to finalize the shape of the glass. The result is a superb conversation starter for any location. Since each piece is created entirely by hand, each glass is unique, baring slight differences from glass to glass. Like all fine art, each and every piece in exclusive and magnificent. Bruck Lighting?s glass, like the Mona Lisa or the Venus Di Milo, is a magnificent, timeless and unique piece of art
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Jacks claim second straight Summit League title
SIOUX FALLS, S.D. - Top-seeded South Dakota State won its second straight Summit League Championships crown on Tuesday with a 73-67 win over No. 3 seed North Dakota State in front of a raucous crowd of 6,544 mostly SDSU fans at the Sioux Falls Arena.
With the win, the Jackrabbits punch their ticket to the NCAA Tournament for the second time in as many years and improve to 25-9 on the season.
"I thought being in the championship game last year was helpful to our players. Last year it felt a little overwhelming and we were very tense and tight in the game, even though we were expected to win it," head coach Scott Nagy said. "NDSU is a tremendous basketball team, particularly with (Taylor) Braun back. They are great defensively, we struggled to get good shots them, and with him back, they're much better offensively. We knew we would have to play tough, we knew we would have to play great defense, and I thought, defensively this was as good as I've seen our guys in a long time."
The Bison, who fall to 24-9 on the season, scored first and after a couple of quick lead changes, opened an early 7-3 lead. The Jacks responded with a 10-0 run to go up 13-7 with 12 minutes and 10 seconds left in the first half, and never trailed again in the game.
Despite not ever trailing again, the Jackrabbits never really pulled away either, as the Bison kept the lead in single digits for the entire half before the Jacks took a 29-25 lead into the locker room.
The SDSU lead reached double figures for the first time at the 16:35 minute mark of the second half on a Brayden Carlson 3-pointer from the left side that put SDSU up 11 points at 36-25. SDSU would push that lead to as many as 12 on a Jordan Dykstra layup and-1 with 11:45 to play.
NDSU came right back with a Braun 3-pointer on the other end, and kept the lead under 10 points for all but a 17 second span between a Nate Wolters jumper at 9:26 that put SDSU up 52-42 and a Mike Felt 3-pointer at the 9:09 mark that cut the lead to 52-45, which started a 10-2 NDSU run that cut the lead to two points 52-52 with 7:24 left in the game.
The Jacks came right back with a quick 8-2 burst to push the lead back to eight points at 62-54 on a pair of Tony Fiegen free throws with 3:39 on the clock. From there, the Jacks went 9-of-10 from the free throw line down the stretch to secure the win.
Wolters led all players with 27 points in the win, adding six each in rebounds and assists in earning tournament MVP honors for the second straight year. A now two-time all-tournament team selection, Dykstra finished with 18 points and seven rebounds, while first-time all-tournament team selection Fiegen finished with 12 points.
Braun, who also earned all-tournament team honors, scored 23 points to lead the Bison. Both TrayVonn Wright and Mike Felt both added nine points in the loss.
Fort Wayne's Frank Gaines rounded out the all-tournament team selections.
The Jackrabbits now wait for an NCAA Tournament opponent, which they learn on Sunday, in a live selection show on CBS at 5 p.m.
NOTES: NDSU leads the all-time series with SDSU 109-98 ... SDSU leads the postseason series tied 3-2 ... Tuesday's game marked the second time SDSU and NDSU met in a conference tournament title game, the first being a 79-75 SDSU win in the North Central Conference Tournament on Feb. 23, 1980 in Brookings ... the win sends South Dakota State to the NCAA Tournament for the 26th time in school history, the second time at the Division I level ... Wolters earned his second consecutive Summit League Championships MVP award after averaging 21.7 points, 4.7 rebounds and 7.3 assists per game ... Wolters scored in double figures for the 71st game in a row and for the 114th time in his career, and scored at least 20 points in game for the 19th time this season and for the 50th time in his career ... Dykstra earned all-tournament team honors for a second straight year, and scored in double figures for the 23rd time this season and for the 58th time in his career ... Fiegen took home all-tournament team honors for the first time after scoring in double figures for the 20th time this season and for the 41st time in his career


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UN.GIFT Publications
Combating Trafficking in Persons in Accordance with the Principles of Islamic Law
Sep 07 2010
Download right click "save as"
This paper addresses principles on the prohibition of exploitation and slavery in both International and Islamic law, as well as principles providing protection for its victims. The paper is targeted both at Islamic practitioners who want to learn more about combating human trafficking and also at anti-trafficking practitioners wanting to learn more about Islamic law.More information about human trafficking on the website of UNODC.
Côte d'IvoireChange TagAll Publications


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Prep time: 5 minutes
Recipe makes: 2 servings
Tip: If you're a babysitter, this is a great recipe to make for kids. Just be sure to ask parents about any food allergies first.
Reviewed by: Meredith Parkinson, RD, LDN
Date reviewed: November 2012
Note: All information is for educational purposes only. For specific medical advice, diagnoses, and treatment, consult your doctor.
© 1995-


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HOME Philadelphia 76ers Gear Philadelphia 76ers Mens Philadelphia 76ers Mens T-Shirts $20 to $40 (46 items) Product ID: 1155622
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Decked out with pixilated graphics looking like they jumped straight off the arcade screen, this NBA Exclusive Collection 8-Bit T-shirt will definitely score you some cool points. NBA team and player text is printed on the chest along with retro game graphics depicting players from the 1982-1983 Philadelphia 76ers.
- 100% Cotton fabric
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- Retro game graphics depicting players from the 1982-1983 Philadelphia 76ers on chest
- Short-sleeved T-shirt
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Master Calendar
Faculty Forum: Diane Lichtenstein
A faculty forum with Diane Lichtenstein.
Date: Wednesday, April 16th, 2014
Time: 12:00 pm
Duration: 1 hour, 20 minutes
Location: Mathers,
Pearsons Hall
Sponsored by: Academic Affairs
Contact: Erica Daniels, email@example.com
A faculty forum with Diane Lichtenstein.
Hot buffet lunch will be available for $3.00 beginning at 12:00 noon. To ensure an accurate count, please RSVP to firstname.lastname@example.com by noon the Monday before the event.
This event is open to faculty and staff.


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Leeper's organic wheat free / gluten free pasta offers full flavor as well as perfect texture. Available in assorted shapes and flavors, this pasta cooks up beautifully. Unlike many rice and corn based pastas, this will not gum up or turn mushy.
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Events Calendar
"The Memorandum," a Beloit College Theatre Production
This event takes place each week on Thursday, Friday and Saturday from November 14th, 2013 to November 23rd, 2013.
Time: 8:00 pm
Duration: 2 hours
Location: Neese Theatre, Neese Complex
Sponsored by: Theatre, Dance and Media Studies
Contact: firstname.lastname@example.com, John Kaufmann 363-2685
Comedy of Bureaucracy
Beloit College will debut its second play of the 2013-14 season with The Memorandum directed by John Kaufmann, assistant professor of theatre arts. This Orwellian gem is set in a model political bureaucracy where a harassed manager unwittingly authorizes an experiment that will introduce a new bureaucratic jargon to supplant the popular language and expedite regimentation.
Admissions: $8.50 ($5 for seniors; $4 for students).
This event is open to campus and community.
This event occurs on:
- Thursday, November 14th, 2013
- Friday, November 15th, 2013
- Saturday, November 16th, 2013
- Thursday, November 21st, 2013
- Friday, November 22nd, 2013
- Saturday, November 23rd, 2013


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Geek Cooked Dinner
From LCA2010
(Difference between revisions)
(→Cookers / Choppers / Minions)
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* ...
* ...
Revision as of 08:22, 20 January 2010
Following the fun and success of last year, we're pondering cooking a dinner @ UStay tonight (Wednesday) - the only spare evening this week. Neatly coincides with Jonathan and Andy doing Arduino soldering in the common room, I'm sure the people involved in that need food too.
If you're interested, please add your name below and state any food prefs/diets so we can work out what to cook and how much! We'll need helpers for chopping stuff, co-funding, etc.
- Level 1 common room, aiming for dinner 6-7pm-ish. BYO booze. If you're not staying at UStay, you'll need to hop along with someone who is, because of the keycard security.
- If you want to help with ingredients purchase, catch me at conf entrance straight after end (5.30pm)
- If you want to help with "menu", catch me during the day.
Cookers / Choppers / Minions
- Arjen - vegetarian but will cook meat for others ;-)
- Shaun Nykvist
- Luke Hovington
- ...


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In general, while we do not share customer information to other third parties, Maternitique will disclose personal user information when required to by law enforcement or other appropriate governmental authorities, or if the personal information is pertinent in a legal proceeding or court action and has been requested of us.
In order to conduct e-commerce functions, Maternitique collects, stores, and in some cases shares, limited customer information as well. Except as required by law (as noted above), the information we share with third parties is used only for the purpose of conducting our business and may include customer names and email addresses. These third party vendors include shipping, search engine optimization and electronic marketing companies. Maternitique partners with them to send you:
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Reason 5: The First Cell
Where did life come from? Either it was created or it came about by accident are really the only two options. Wait!, someone might respond, what if it came from outer space, what if we were seeded by alien beings? The alien seeding is only removing the argument from this world and sending it to another. Because the follow up question is what caused the alien life?
Ezekiel Chapter 38, Gog Prince of Rus (Russia) of the land of Magog.
The book of Ezekiel foretells a day after Israel is gathered from the nations in the "Last Days" how the an invasion from the North will be defeated by God. The armies involve an Russian and Islamic invasion against the land of Israel.
God defeats these nations to demonstrate to the world his Holiness and the evidence of His Word.
After Russia and Israel are defeated, the nation of Israel will build the Third Temple, bringing the "Tribulation" on the whole world.
The Seventy Weeks of Daniel
Almost 2600-years ago, the prophet Daniel in the Bible foretold of events that would impact the whole world. Daniel foretold the exact time Jesus time to the day, Israel would reject and kill Jesus, he foretold the destruction of the 2nd Temple after the death of Messiah. Daniel established the blueprint of Bible Prophecy, showing how in the "Last Days" a third Temple would be the focus of world attention.
We are living in those days as Israel has plans to build the Third Temple on the site of Islam's 3rd most holy location, the Dome of the Rock.
Islam is according to some the fastest growing religion in the world today. Over 20% of the Earth's population is Muslim, so its important to understand this large group of people. In this article we will cover the world before Islam, the history of Mohammad and the history of Islam. The Quran, Hadith and the Bible are also explained in how they relate to the Islamic faith.
Another aspect of Islam is how it relates to Judaism and Christianity, since it looks to both religions as connected to the prophets.
Ephesians Chapter 2:11-21 God's Amazing Grace
Do we really know how awesome and amazing our salvation is? For many of us, raised in the church and with Christian friends, it is easy to become complacent and desensitized to our salvation. We see ourselves as good people who go to church Sunday, not realizing how we were rescued from the depths of depravity. God has taken us from a point of spiritual death, elevating us to "Sonship", with all of Heaven as our inheritance. We will never really understand our amazing salvation until we see the reality of it in Heaven.
Islam and Israel an Introduction
The linking of the nation of Israel with the emergence of Islam as a major world religion, encompassing over 20% of the earth's population is just a coincidence to some. However, for those who know Bible Prophecy there is no such thing. Central to the scripture is God's
prophetic plan for the nation of Israel and the Jewish people.
To understand these amazing circumstances, we need to comprehend the emergence of the nation of Israel in 1948, a recent event. Prior to this period, the last
A Study of Psalm 83
If you want to understand what is going to happen in the Middle East, all you have to do is turn to Psalm 83. This Psalm was written by Asaph, under the inspiration of the Holy Spirit, to reveal an event which is now being fulfilled. Asaph was Levite and prophet who composed 11 Psalms (Psalms 72-83) in the time of David (I Chronicles 6:39). Asaph wrote about a day in which all the surrounding nations would conspire with one mind to eliminate Israel from being a nation.


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A Review of: Dorit Baxter Day Spa
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Indoor surfing, spinning
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- Windsor
Welcome to the most comprehesive list of real estate agents and real estate offices in Ontario. This list of agents will help you find an real estate agent quickly and with more confidence.
We strive to have a comprehensive list of real estate companies in Windsor. If you are a real estate agent missing from our list. Please signup today. It is free!


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Barry Woodrow Fouraker, 49, died July 11, 2012, the result of an auto accident. He was a resident of Bryceville and Tallahassee for many years, and was a wonderful father and loving husband, as well as an avid lover of all things outdoors. Barry was preceded in death by his father Lester Fouraker.
Survivors include wife Kelly; daughters Stephanie, Madison and Catie; mother Judy; brothers Arthur (Mary) and Rhett (Machelle); sisters Mia Abernathy (Paul) and Amanda Baines; many nieces, nephews, aunts, uncles, cousins and friends.


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The Biopython Structural Bioinformatics FAQ
m (→Can I access the header information?)
(→How do I keep a local copy of the PDB up-to-date?)
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pl = PDBList(pdb='/data/pdb')
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during the current week. For more info on the possibilities of PDBList,
during the current week. For more info on the possibilities of PDBList,
see the API documentation.
see the API documentation.
==== What about all those buggy PDB files? ====
==== What about all those buggy PDB files? ====
Revision as of 03:06, 26 March 2013
Bio.PDB is a biopython module that focuses on working with crystal structures of biological macromolecules. This document gives a fairly complete overview of Bio.PDB.
Bio.PDB's installation
Bio.PDB is automatically installed as part of Biopython. Biopython can be obtained from http://www.biopython.org. It runs on many platforms (Linux/Unix, windows, Mac,...).
Who's using Bio.PDB?
Bio.PDB was used in the construction of DISEMBL, a web server that predicts disordered regions in proteins (http://dis.embl.de/), and COLUMBA, a website that provides annotated protein structures (http://www.columba-db.de/). Bio.PDB has also been used to perform a large scale search for active sites similarities between protein structures in the PDB (see [http://dx.doi.org/10.1002/prot.10338 \textit{Proteins Struct. Func. Gen., \textbf{2003, 51, 96-108]) , and to develop a new algorithm that identifies linear secondary structure elements ([\emph{BMC Bioinformatics, \textbf{2005, 6, 202 http://www.biomedcentral.com/1471-2105/6/202]).
Judging from requests for features and information, Bio.PDB is also used by several LPCs (Large Pharmaceutical Companies :-).
Is there a Bio.PDB reference?
Yes, and I'd appreciate it if you would refer to Bio.PDB in publications if you make use of it. The reference is:
\begin{quote Hamelryck, T., Manderick, B. (2003) PDB parser and structure class implemented in Python. \textit{Bioinformatics, \textbf{19, 2308-2310. \end{quote The article can be freely downloaded via the Bioinformatics journal website (http://www.binf.ku.dk/users/thamelry/references.html). I welcome e-mails telling me what you are using Bio.PDB for. Feature requests are welcome too.
How well tested is Bio.PDB?
Pretty well, actually. Bio.PDB has been extensively tested on nearly 5500 structures from the PDB - all structures seemed to be parsed correctly. More details can be found in the Bio.PDB Bioinformatics article. Bio.PDB has been used/is being used in many research projects as a reliable tool. In fact, I'm using Bio.PDB almost daily for research purposes and continue working on improving it and adding new features.
How fast is it?
PDBParser performance was tested on about 800 structures
(each belonging to a unique SCOP superfamily). This takes about 20
minutes, or on average 1.5 seconds per structure. Parsing the structure
of the large ribosomal subunit (1FKK), which contains about 64000
atoms, takes 10 seconds on a 1000 MHz PC. In short: it's more than
fast enough for many applications.
Why should I use Bio.PDB?
Bio.PDB might be exactly what you want, and then again it might not. If you are interested in data mining the PDB header, you might want to look elsewhere because there is only limited support for this. If you look for a powerful, complete data structure to access the atomic data Bio.PDB is probably for you.
General questions
Importing Bio.PDB
That's simple:
from Bio.PDB import *
Is there support for molecular graphics?
Not directly, mostly since there are quite a few Python based/Python aware solutions already, that can potentially be used with Bio.PDB. My choice is Pymol, BTW (I've used this successfully with Bio.PDB, and there will probably be specific PyMol modules in Bio.PDB soon/some day). Python based/aware molecular graphics solutions include:
- PyMol: http://pymol.sourceforge.net/
- Chimera: http://www.cgl.ucsf.edu/chimera/
- PMV: http://www.scripps.edu/ sanner/python/
- Coot: http://www.ysbl.york.ac.uk/ emsley/coot/
- CCP4mg: http://www.ysbl.york.ac.uk/ lizp/molgraphics.html
- mmLib: http://pymmlib.sourceforge.net/
- VMD: http://www.ks.uiuc.edu/Research/vmd/
- MMTK: http://starship.python.net/crew/hinsen/MMTK/
I'd be crazy to write another molecular graphics application (been there - done that, actually :-).
How do I create a structure object from a PDB file?
First, create a
PDBParser object:
parser = PDBParser()
Then, create a structure object from a PDB file in the following way (the PDB file in this case is called '1FAT.pdb', 'PHA-L' is a user defined name for the structure):
structure = parser.get_structure('PHA-L', '1FAT.pdb')
How do I create a structure object from an mmCIF file?
Similarly to the case the case of PDB files, first create an
parser = MMCIFParser()
Then use this parser to create a structure object from the mmCIF file:
structure = parser.get_structure('PHA-L', '1FAT.cif')
...and what about the new PDB XML format?
That's not yet supported, but I'm definitely planning to support that in the future (it's not a lot of work). Contact me if you need this, it might encourage me :-).
I'd like to have some more low level access to an mmCIF file...
You got it. You can create a python dictionary that maps all mmCIF
tags in an mmCIF file to their values. If there are multiple values
(like in the case of tag
_atom_site.Cartn_y, which holds
the y coordinates of all atoms), the tag is mapped to a list of values.
The dictionary is created from the mmCIF file as follows:
mmcif_dict = MMCIF2Dict('1FAT.cif')
Example: get the solvent content from an mmCIF file:
sc = mmcif_dict['_exptl_crystal.density_percent_sol']
Example: get the list of the y coordinates of all atoms
y_list = mmcif_dict['_atom_site.Cartn_y']
Can I access the header information?
Thanks to Christian Rother you can access some information from the
PDB header. Note however that many PDB files contain headers with
incomplete or erroneous information. Many of the errors have been
fixed in the equivalent mmCIF files.
Hence, if you are interested in the header information, it is a good idea to extract information from mmCIF files using the
MMCIF2Dict tool described above, instead of parsing the PDB header.
Now that is clarified, let's return to parsing the PDB header. The
structure object has an attribute called
header which is
a python dictionary that maps header records to their values.
resolution = structure.header['resolution'] keywords = structure.header['keywords']
The available keys are
structure_reference (maps to
a list of references),
author and
compound (maps to a dictionary with various information about
the crystallized compound).
The dictionary can also be created without creating a
object, ie. directly from the PDB file:
handle = open(filename,'r') header_dict = parse_pdb_header(handle) handle.close()
Can I use Bio.PDB with NMR structures (ie. with more than one model)?
Sure. Many PDB parsers assume that there is only one model, making
them all but useless for NMR structures. The design of the
object makes it easy to handle PDB files with more than one model
(see section #The Structure object).
How do I download structures from the PDB?
This can be done using the
PDBList object, using the
method. The argument for this method is the PDB identifier of the
pdbl = PDBList() pdbl.retrieve_pdb_file('1FAT')
PDBList class can also be used as a command-line tool:
python PDBList.py 1fat
The downloaded file will be called
pdb1fat.ent and stored
in the current working directory. Note that the
method also has an optional argument
pdir that specifies
a specific directory in which to store the downloaded PDB files.
retrieve_pdb_file method also has some options for specifying
the compression format used for the download, and the program used
for local decompression (default
.Z format and
In addition, the PDB ftp site can be specified upon creation of the
PDBList object. By default, the server of the Worldwide Protein Data Bank (\url{ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/})
is used. See the API documentation for more details. Thanks again
to Kristian Rother for donating this module.
How do I download the entire PDB?
The following commands will store all PDB files in the
python PDBList.py all /data/pdb
python PDBList.py all /data/pdb -d
The API method for this is called
Adding the
-d option will store all files in the same directory.
Otherwise, they are sorted into PDB-style subdirectories according
to their PDB ID's. Depending on the traffic, a complete download will
take 2-4 days.
How do I keep a local copy of the PDB up-to-date?
This can also be done using the
PDBList object. One simply
creates a
PDBList object (specifying the directory where
the local copy of the PDB is present) and calls the
pl = PDBList(pdb='/data/pdb') pl.update_pdb()
One can of course make a weekly cronjob out of this to keep the local copy automatically up-to-date. The PDB ftp site can also be specified (see API documentation).
PDBList has some additional methods that can be of use. The
get_all_obsolete method can be used to get a list of all
obsolete PDB entries. The
changed_this_week method can
be used to obtain the entries that were added, modified or obsoleted
during the current week. For more info on the possibilities of
see the API documentation.
What about all those buggy PDB files?
It is well known that many PDB files contain semantic errors (I'm not talking about the structures themselves know, but their representation in PDB files). Bio.PDB tries to handle this in two ways. The PDBParser object can behave in two ways: a restrictive way and a permissive way (THIS IS NOW THE DEFAULT). The restrictive way used to be the default, but people seemed to think that Bio.PDB 'crashed' due to a bug (hah!), so I changed it. If you ever encounter a real bug, please tell me immediately!
\# Permissive parser parser=PDBParser(PERMISSIVE=1) parser=PDBParser() \# The same (default) \# Strict parser strict_parser=PDBParser(PERMISSIVE=0)
In the permissive state (DEFAULT), PDB files that obviously contain errors are 'corrected' (ie. some residues or atoms are left out). These errors include:
\begin{itemize \item Multiple residues with the same identifier \item Multiple atoms with the same identifier (taking into account the altloc identifier) \end{itemize These errors indicate real problems in the PDB file (for details see the Bioinformatics article). In the restrictive state, PDB files with errors cause an exception to occur. This is useful to find errors in PDB files.
Some errors however are automatically corrected. Normally each disordered atom should have a non-blanc altloc identifier. However, there are many structures that do not follow this convention, and have a blank and a non-blank identifier for two disordered positions of the same atom. This is automatically interpreted in the right way.
Sometimes a structure contains a list of residues belonging to chain A, followed by residues belonging to chain B, and again followed by residues belonging to chain A, i.e. the chains are 'broken'. This is also correctly interpreted.
Can I write PDB files?
Use the PDBIO class for this. It's easy to write out specific parts of a structure too, of course.
Example: saving a structure
io=PDBIO() io.set_structure(s) io.save('out.pdb')
If you want to write out a part of the structure, make use of the
Select class (also in
PDBIO). Select has four methods:
accept_model(model) accept_chain(chain) accept_residue(residue) accept_atom(atom)
By default, every method returns 1 (which means the model/chain/residue/atom
is included in the output). By subclassing
Select and returning
0 when appropriate you can exclude models, chains, etc. from the output.
Cumbersome maybe, but very powerful. The following code only writes
out glycine residues:
class GlySelect(Select): def accept_residue(self, residue): if residue.get_name()=='GLY': return 1 else: return 0 io=PDBIO() io.set_structure(s) io.save('gly_only.pdb', GlySelect())
If this is all too complicated for you, the
Dice module contains
a handy
extract function that writes out all residues in
a chain between a start and end residue.
Can I write mmCIF files?
No, and I also don't have plans to add that functionality soon (or ever - I don't need it at all, and it's a lot of work, plus no-one has ever asked for it). People who want to add this can contact me.
The Structure object
What's the overall layout of a Structure object?
Structure object follows the so-called SMCRA
(Structure/Model/Chain/Residue/Atom) architecture :
\item A structure consists of models
\item A model consists of chains
\item A chain consists of residues
\item A residue consists of atoms
This is the way many structural biologists/bioinformaticians think
about structure, and provides a simple but efficient way to deal with
structure. Additional stuff is essentially added when needed. A UML
diagram of the
Structure object (forget about the
classes for now) is shown in Fig. \ref{cap:SMCRA.
% \begin{figure[tbh] \begin{center\includegraphics[%
width=100mm, keepaspectratio]{images/smcra.png\end{center
\caption{\label{cap:SMCRAUML diagram of SMCRA architecture of the
object. Full lines with diamonds denote aggregation, full lines with
arrows denote referencing, full lines with triangles denote inheritance
and dashed lines with triangles denote interface realization.
The following code iterates through all atoms of a structure:
p=PDBParser() structure=p.get_structure('X', 'pdb1fat.ent') for model in structure: for chain in model: for residue in chain: for atom in residue: print atom
There are also some shortcuts:
\# Iterate over all atoms in a structure for atom in structure.get_atoms(): print atom \# Iterate over all residues in a model for residue in model.get_residues(): print residue
Structures, models, chains, residues and atoms are called
in Biopython. You can always get a parent
Entity from a child
Entity, eg.:
residue=atom.get_parent() chain=residue.get_parent()
You can also test whether an
Entity has a certain child using
has_id method.
Can I do that a bit more conveniently?
You can do things like:
atoms=structure.get_atoms() residue=structure.get_residues() atoms=chain.get_atoms()
You can also use the
Selection.unfold_entities function:
\# Get all residues from a structure res_list=Selection.unfold_entities(structure, 'R') \# Get all atoms from a chain atom_list=Selection.unfold_entities(chain, 'A')
A=atom, R=residue, C=chain, M=model, S=structure.
You can use this to go up in the hierarchy, eg.\ to get a list of
Residue or
Chain parents from a list of
residue_list=Selection.unfold_entities(atom_list, 'R') chain_list=Selection.unfold_entities(atom_list, 'C')
For more info, see the API documentation.
==== How do I extract a specific
from a
Structure? ====
Easy. Here are some examples:
model=structure{[0{] chain=model{['A'{] residue=chain{[100{] atom=residue{['CA'{]
Note that you can use a shortcut:
What is a model id?
The model id is an integer which denotes the rank of the model in the PDB/mmCIF file. The model is starts at 0. Crystal structures generally have only one model (with id 0), while NMR files usually have several models.
What is a chain id?
The chain id is specified in the PDB/mmCIF file, and is a single character (typically a letter).
What is a residue id?
This is a bit more complicated, due to the clumsy PDB format. A residue id is a tuple with three elements:
\item The \textbf{hetero-flag: this is
'H_' plus the name of
the hetero-residue (eg.
'H_GLC' in the case of a glucose
molecule), or
'W' in the case of a water molecule.
\item The \textbf{sequence identifier in the chain, eg. 100
\item The \textbf{insertion code, eg. 'A'. The insertion code is sometimes
used to preserve a certain desirable residue numbering scheme. A Ser
80 insertion mutant (inserted e.g. between a Thr 80 and an Asn 81
residue) could e.g. have sequence identifiers and insertion codes
as follows: Thr 80 A, Ser 80 B, Asn 81. In this way the residue numbering
scheme stays in tune with that of the wild type structure.
The id of the above glucose residue would thus be
100, 'A'). If the hetero-flag and insertion code are blank, the sequence
identifier alone can be used:
\# Full id residue=chain{[(' ', 100, ' '){] \# Shortcut id residue=chain{[100{]
The reason for the hetero-flag is that many, many PDB files use the same sequence identifier for an amino acid and a hetero-residue or a water, which would create obvious problems if the hetero-flag was not used.
What is an atom id?
The atom id is simply the atom name (eg.
'CA'). In practice,
the atom name is created by stripping all spaces from the atom name
in the PDB file.
However, in PDB files, a space can be part of an atom name. Often,
calcium atoms are called
'CA..' in order to distinguish them
from C$\alpha$ atoms (which are called
'.CA.'). In cases
were stripping the spaces would create problems (ie. two atoms called
'CA' in the same residue) the spaces are kept.
How is disorder handled?
This is one of the strong points of Bio.PDB. It can handle both disordered atoms and point mutations (ie. a Gly and an Ala residue in the same position).
Disorder should be dealt with from two points of view: the atom and the residue points of view. In general, I have tried to encapsulate all the complexity that arises from disorder. If you just want to loop over all C$\alpha$ atoms, you do not care that some residues have a disordered side chain. On the other hand it should also be possible to represent disorder completely in the data structure. Therefore, disordered atoms or residues are stored in special objects that behave as if there is no disorder. This is done by only representing a subset of the disordered atoms or residues. Which subset is picked (e.g. which of the two disordered OG side chain atom positions of a Ser residue is used) can be specified by the user.
\textbf{Disordered atom positions are represented by ordinary
objects, but all
Atom objects that represent the same physical
atom are stored in a
DisorderedAtom object (see Fig. \ref{cap:SMCRA).
Atom object in a
DisorderedAtom object can
be uniquely indexed using its altloc specifier. The
object forwards all uncaught method calls to the selected Atom object,
by default the one that represents the atom with the highest
occupancy. The user can of course change the selected
object, making use of its altloc specifier. In this way atom disorder
is represented correctly without much additional complexity. In other
words, if you are not interested in atom disorder, you will not be
bothered by it.
Each disordered atom has a characteristic altloc identifier. You can
specify that a
DisorderedAtom object should behave like
Atom object associated with a specific altloc identifier:
atom.disordered_select('A') \# select altloc A atom atom.disordered_select('B') \# select altloc B atom
A special case arises when disorder is due to \textbf{point mutations, i.e. when two or more point mutants of a polypeptide are present in the crystal. An example of this can be found in PDB structure 1EN2.
Since these residues belong to a different residue type (e.g. let's
say Ser 60 and Cys 60) they should not be stored in a single
object as in the common case. In this case, each residue is represented
by one
Residue object, and both
Residue objects
are stored in a single
DisorderedResidue object (see Fig.
DisorderedResidue object forwards all uncaught
methods to the selected
Residue object (by default the last
Residue object added), and thus behaves like an ordinary
residue. Each
Residue object in a
object can be uniquely identified by its residue name. In the above
example, residue Ser 60 would have id 'SER' in the
object, while residue Cys 60 would have id 'CYS'. The user can select
the active
Residue object in a
object via this id.
Example: suppose that a chain has a point mutation at position 10, consisting of a Ser and a Cys residue. Make sure that residue 10 of this chain behaves as the Cys residue.
residue=chain{[10{] residue.disordered_select('CYS')
In addition, you can get a list of all
Atom objects (ie.
DisorderedAtom objects are 'unpacked' to their individual
Atom objects) using the
get_unpacked_list method
of a (
Residue object.
Can I sort residues in a chain somehow?
Yes, kinda, but I'm waiting for a request for this feature to finish it :-).
How are ligands and solvent handled?
See 'What is a residue id?'.
What about B factors?
Well, yes! Bio.PDB supports isotropic and anisotropic B factors, and also deals with standard deviations of anisotropic B factor if present (see the section #Analysis).
What about standard deviation of atomic positions?
Yup, supported. See the section #Analysis.
==== I think the SMCRA data structure is not flexible/sexy/whatever enough... ====
Sure, sure. Everybody is always coming up with (mostly vaporware or partly implemented) data structures that handle all possible situations and are extensible in all thinkable (and unthinkable) ways. The prosaic truth however is that 99.9\% of people using (and I mean really using!) crystal structures think in terms of models, chains, residues and atoms. The philosophy of Bio.PDB is to provide a reasonably fast, clean, simple, but complete data structure to access structure data. The proof of the pudding is in the eating.
Moreover, it is quite easy to build more specialised data structures
on top of the
Structure class (eg. there's a
class). On the other hand, the
Structure object is built
using a Parser/Consumer approach (called
StructureBuilder, respectively). One can easily reuse
the PDB/mmCIF parsers by implementing a specialised
class. It is of course also trivial to add support for new file formats
by writing new parsers.
How do I extract information from an
Atom object?
Using the following methods:
a.get_name() \# atom name (spaces stripped, e.g. 'CA') a.get_id() \# id (equals atom name) a.get_coord() \# atomic coordinates a.get_vector() \# atomic coordinates as Vector object a.get_bfactor() \# isotropic B factor a.get_occupancy() \# occupancy a.get_altloc() \# alternative location specifier a.get_sigatm() \# std. dev. of atomic parameters a.get_siguij() \# std. dev. of anisotropic B factor a.get_anisou() \# anisotropic B factor a.get_fullname() \# atom name (with spaces, e.g. '.CA.')
How do I extract information from a
Residue object?
Using the following methods:
r.get_resname() \# return the residue name (eg. 'GLY') r.is_disordered() \# 1 if the residue has disordered atoms r.get_segid() \# return the SEGID r.has_id(name) \# test if a residue has a certain atom
How do I measure distances?
That's simple: the minus operator for atoms has been overloaded to return the distance between two atoms.
\# Get some atoms ca1=residue1{['CA'{] ca2=residue2{['CA'{] \# Simply subtract the atoms to get their distance distance=ca1-ca2
How do I measure angles?
This can easily be done via the vector representation of the atomic
coordinates, and the
calc_angle function from the
vector1=atom1.get_vector() vector2=atom2.get_vector() vector3=atom3.get_vector() angle=calc_angle(vector1, vector2, vector3)
How do I measure torsion angles?
Again, this can easily be done via the vector representation of the
atomic coordinates, this time using the
calc_dihedral function
from the
Vector module:
vector1=atom1.get_vector() vector2=atom2.get_vector() vector3=atom3.get_vector() vector4=atom4.get_vector() angle=calc_dihedral(vector1, vector2, vector3, vector4)
How do I determine atom-atom contacts?
NeighborSearch. This uses a KD tree data structure coded
in C behind the screens, so it's pretty darn fast (see
How do I extract polypeptides from a
Structure object?
PolypeptideBuilder. You can use the resulting
object to get the sequence as a
Seq object or to get a list
of C$\alpha$ atoms as well. Polypeptides can be built using a C-N
or a C$\alpha$-C$\alpha$ distance criterion.
\# Using C-N ppb=PPBuilder() for pp in ppb.build_peptides(structure): print pp.get_sequence() \# Using CA-CA ppb=CaPPBuilder() for pp in ppb.build_peptides(structure): print pp.get_sequence()
Note that in the above case only model 0 of the structure is considered
PolypeptideBuilder. However, it is possible to use
to build
Polypeptide objects from
Model and
objects as well.
How do I get the sequence of a structure?
The first thing to do is to extract all polypeptides from the structure
(see previous entry). The sequence of each polypeptide can then easily
be obtained from the
Polypeptide objects. The sequence is
represented as a Biopython
Seq object, and its alphabet is
defined by a
ProteinAlphabet object.
>\,{>\,{> seq=polypeptide.get_sequence() >\,{>\,{> print seq Seq('SNVVE...', <class Bio.Alphabet.ProteinAlphabet>)
How do I determine secondary structure?
For this functionality, you need to install DSSP (and obtain a license
for it - free for academic use, see http://www.cmbi.kun.nl/gv/dssp/).
Then use the
DSSP class, which maps
Residue objects
to their secondary structure (and accessible surface area). The DSSP
codes are listed in Table \ref{cap:DSSP-codes. Note that DSSP (the
program, and thus by consequence the class) cannot handle multiple
% \begin{table
==== \begin{tabular{|c|c| \hline Code& Secondary structure\tabularnewline \hline \hline H& $\alpha$-helix\tabularnewline \hline B& Isolated $\beta$-bridge residue\tabularnewline \hline E& Strand \tabularnewline \hline G& 3-10 helix \tabularnewline \hline I& $\Pi$-helix \tabularnewline \hline T& Turn\tabularnewline \hline S& Bend \tabularnewline \hline -& Other\tabularnewline \hline \end{tabular
\caption{\label{cap:DSSP-codesDSSP codes in Bio.PDB. \end{table
How do I calculate the accessible surface area of a residue?
Use the
DSSP class (see also previous entry). But see also
next entry.
How do I calculate residue depth?
Residue depth is the average distance of a residue's atoms from the
solvent accessible surface. It's a fairly new and very powerful parameterization
of solvent accessibility. For this functionality, you need to install
Michel Sanner's MSMS program (http://www.scripps.edu/pub/olson-web/people/sanner/html/msms_home.html).
Then use the
ResidueDepth class. This class behaves as a
dictionary which maps
Residue objects to corresponding (residue
depth, C$\alpha$ depth) tuples. The C$\alpha$ depth is the distance
of a residue's C$\alpha$ atom to the solvent accessible surface.
model = structure[0] rd = ResidueDepth(model, pdb_file) residue_depth, ca_depth=rd[some_residue]
You can also get access to the molecular surface itself (via the
function), in the form of a Numeric python array with the surface points.
How do I calculate Half Sphere Exposure?
Half Sphere Exposure (HSE) is a new, 2D measure of solvent exposure. Basically, it counts the number of C$\alpha$ atoms around a residue in the direction of its side chain, and in the opposite direction (within a radius of 13 Å). Despite its simplicity, it outperforms many other measures of solvent exposure. An article describing this novel 2D measure has been submitted.
HSE comes in two flavors: HSE$\alpha$ and HSE$\beta$. The former
only uses the C$\alpha$ atom positions, while the latter uses the
C$\alpha$ and C$\beta$ atom positions. The HSE measure is calculated
by the
HSExposure class, which can also calculate the contact
number. The latter class has methods which return dictionaries that
map a
Residue object to its corresponding HSE$\alpha$, HSE$\beta$
and contact number values.
model=structure[0] hse=HSExposure() \# Calculate HSEalpha exp_ca=hse.calc_hs_exposure(model, option='CA3') \# Calculate HSEbeta exp_cb=hse.calc_hs_exposure(model, option='CB') \# Calculate classical coordination number exp_fs=hse.calc_fs_exposure(model) \# Print HSEalpha for a residue print exp_ca{[some_residue{]
First, create an alignment file in FASTA format, then use the
class. This class can also be used for alignments with more than two
How do I test if a Residue object is an amino acid?
Can I do vector operations on atomic coordinates?
Atom objects return a
Vector object representation
of the coordinates with the
get_vector method.
implements the full set of 3D vector operations, matrix multiplication
(left and right) and some advanced rotation-related operations as
well. See also next question.
How do I put a virtual C$\beta$ on a Gly residue?
OK, I admit, this example is only present to show off the possibilities
of Bio.PDB's
Vector module (though this code is actually
used in the
HSExposure module, which contains a novel way
to parametrize residue exposure - publication underway). Suppose that
you would like to find the position of a Gly residue's C$\beta$ atom,
if it had one. How would you do that? Well, rotating the N atom of
the Gly residue along the C$\alpha$-C bond over -120 degrees roughly
puts it in the position of a virtual C$\beta$ atom. Here's how to
do it, making use of the
rotaxis method (which can be used
to construct a rotation around a certain axis) of the
\# get atom coordinates as vectors n=residue{['N'{].get_vector() c=residue{['C'{].get_vector() ca=residue{['CA'{].get_vector() \# center at origin n=n-ca c=c-ca \# find rotation matrix that rotates n \# -120 degrees along the ca-c vector rot=rotaxis(-pi{*120.0/180.0, c) \# apply rotation to ca-n vector cb_at_origin=n.left_multiply(rot) \# put on top of ca atom cb=cb_at_origin+ca
This example shows that it's possible to do some quite nontrivial
vector operations on atomic data, which can be quite useful. In addition
to all the usual vector operations (cross (use
**), and
dot (use
*) product, angle, norm, etc.) and the above mentioned
rotaxis function, the Vector module also has methods
to rotate (rotmat) or reflect (
refmat) one vector
on top of another.
Manipulating the structure
How do I superimpose two structures?
Surprisingly, this is done using the
Superimposer object.
This object calculates the rotation and translation matrix that rotates
two lists of atoms on top of each other in such a way that their RMSD
is minimized. Of course, the two lists need to contain the same amount
of atoms. The
Superimposer object can also apply the rotation/translation
to a list of atoms. The rotation and translation are stored as a tuple
in the
rotran attribute of the
Superimposer object
(note that the rotation is right multiplying!). The RMSD is stored
in the
rmsd attribute.
The algorithm used by
Superimposer comes from \textit{Matrix
computations, 2nd ed. Golub, G. \& Van Loan (1989) and makes use
of singular value decomposition (this is implemented in the general
Bio.SVDSuperimposer module).
sup=Superimposer() \# Specify the atom lists \# 'fixed' and 'moving' are lists of Atom objects \# The moving atoms will be put on the fixed atoms sup.set_atoms(fixed, moving) \# Print rotation/translation/rmsd print sup.rotran print sup.rms \# Apply rotation/translation to the moving atoms sup.apply(moving)
How do I superimpose two structures based on their active sites?
Pretty easily. Use the active site atoms to calculate the rotation/translation matrices (see above), and apply these to the whole molecule.
Can I manipulate the atomic coordinates?
Yes, using the
transform method of the
Atom object,
or directly using the
set_coord method.
Other Structural Bioinformatics modules
See the main Biopython tutorial.
No documentation available yet.
You haven't answered my question yet!
Woah! It's late and I'm tired, and a glass of excellent Pedro Ximenez sherry is waiting for me. Just drop me a mail, and I'll answer you in the morning (with a bit of luck...).
The main author/maintainer of Bio.PDB is:
Thomas Hamelryck Bioinformatics center Institute of Molecular Biology University of Copenhagen Universitetsparken 15, Bygning 10 DK-2100 København Ø Denmark email@example.com
Kristian Rother donated code to interact with the PDB database, and to parse the PDB
header. Indraneel Majumdar sent in some bug reports and assisted in
coding the
Polypeptide module. Many thanks to Brad Chapman,
Jeffrey Chang, Andrew Dalke and Iddo Friedberg for suggestions, comments,
help and/or biting criticism :-).
Can I contribute?
Yes, yes, yes! Just send me an e-mail (email@example.com) or to the Biopython developers (firstname.lastname@example.com) if you have something useful to contribute! Eternal fame awaits!


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This is the 2nd set I've had fitted to my 99T reg Honda Prelude 2.0L ~ 140bhp, done 50k (yes 50,000 miles) on my first set, 10k on the front, 40k on the back. Still had almost 3mm tread left, but the weather was changing, so decided to replace them. At £107 each for 205/50R16's I thought they were good value. They replaced some Falken FK452's that only did about 19k on the front, 22k mixture of front & back. I'd guess the Conti's would do at least 30k if you didn't rotate them, on the front.21/09/2013
These tyres suit this car - I have one original tyre still on the car rear axle after 36000 miles!! Definitely replace with the same model!19/06/2012
Excellent Braking and Wet weather performance. Reasonable wear too.05/06/2012
Excellent grip and super quiet16/04/2012
These tyres did 29, 540 miles on the FRONT of my FWD Audi A4 TDI (140). Grip was always good, even in the wet. I only replaced them as they were down to about 2-3mm and there was snow forecast!03/11/2011
Customer Ratings
Number of ratings: 2
- Car feels better to drive:
- Would buy again:
- Value for money:
- Overall rating:
- Excellent handling in both dry and wet conditions.
- Superb braking performance.
- Outstanding traction.
- Boasts good levels of comfort and low levels of road noise.


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Prices and availability are subject to change from the time and date that you print this page.
2/9/2016 11:14:22 AM. For Customer Service, please call 800.933.9904
$8.97reg. $29.00
Featuring two-tone shades and a variety of colors to choose from, our Lighten Up Floor Shade will certainly brighten your mood and your room.
Details, details
- Nod exclusive
- Base and shade sold separately
- Shade is compatible with all individually sold floor bases from the Land of Nod
- Can be used with base that accommodates a 23W CFL max. bulb (100W incandescent max.) learn more
- Shade does not have or accommodate a harp
- Polarized plug, clear cord, socket switch
- UL-listed learn more
- More colors available
Show 'em what you're made of
- Cotton fabric with styrene backing, metal spider
The Land of Nod Guarantee
At The Land of Nod, nothing is more important to us than providing safe, high-quality products to you and your family. We believe that kids' products should be able to handle everything kids throw their way (literally and figuratively). That's why all of our products have an 18-year quality guarantee. And, hopefully, your kids will no longer be sleeping in bunk beds by then.
Knock, Knock.
Who's there?
Water who?
Water you doing in my house?
Who's there?
Water who?
Water you doing in my house?
Floor Shade
Light Years Lamp Base
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Floral Gem Bedding $14.97 - $89.97reg. $19.00 - $109.00
Ink Spot Rug (Blue) $249.00 - $699.00More Colors Available
Welcome to the Jungle Bedding $19.00 - $169.00
Periscope Floor Lamp $199.00


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Main Content
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The world is your playground, so take yourself to new places with this Compass backpack from Alpinestars. When it comes to backpacks, it doesn't get any better than this. Made of glossy polyester twill that's sure to garner some attention, this bad boy features an embroidered A-stars logo at the top, a debossed A-stars logo at the faux leather top carry handle, a front organizer compartment with multiple padded slots, a large main compartment with a laptop pocket, custom A-stars zipper pulls, side pockets and a headphone port for your music player.
- 100% Polyester twill
- Airmesh back padding
- Alpinestars embroidery
- Alpinestars screen print
- Alpinestars zipper pulls
- Imported
- iPad/Macbook Air 11" Pocket
- Large main compartment
- Measures approximately 12" x 8" x 19"
- Media pocket
- Media port
- Mesh cable pouch
- Padded laptop compartment
- Personal gaming system pocket
- Zippered side pockets
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Six county commission candidates, two of whom will be on the primary ballot on August 14, fielded a host of questions during a forum held at the high school on July 28 before a crowd of more than 100 civic-minded constituents.
Lucy and David Hudson traveled from Olustee to attend the more than two-hour forum, which also included candidates for school board and sheriff [see related article on school board forum here].
The couple said prior to the start they wanted to become more informed voters and hoped to hear more about the candidate's budget priorities.
"We have so little money in the county budget and so many things that need to be done, how are they going to set the priorities?" Mr. Hudson asked rhetorically. "It's going to be very, very hard."
Soon after delivering their opening statements, the candidate were asked about the county's budget woes.