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How to efficiently change background color with GIMP

9/18/2014

9 Comments

 
This tutorial shows you how you can efficiently replace the background of an image with another in GIMP, through the use of the color to alpha plug-in, which is very effective in selecting the image from the backgroung.

1.
The first step is to activate the color to alpha plug-in. Its menu location is <image> Filters -> Colors -> Color To Alpha, where <image> means to right click on the image. If its grayed-out, it means that you have an indexed image. If its not there, upgrade your gimp to 1.2.x.

2.
Next use the Color Picker Tool to select the background color. Or just open the toolbox (Tool -> Toolbox) and choose the background color from the last image. Then choose Layer -> Create New Layer, and choose "Foreground color".

3. (Optional)
When you used the color picker to select the background, a window with the color popped up. Click, hold, and drag from the color portion of this window to the color portion of the Color To Alpha plug-in. If using Gimp for Windows, you'll have to right-click on the destination button and select the Foreground - drag n' drop doesn't work. Click OK after the color indicator on the Color To Alpha plug-in is changed to blue. Alternatively, make sure that the "color to alpha" is selected when you did Step 1.

4.
Now create a New Layer as a Background. The background will now come on top of your image, but don't worry because your image is just layered beneath. Choose "Layer -> Stack -> Reverse Layer Order".

5. Remove the layers: Image -> Flatten.

6. If you want to change your image resolution, do:
Image>Print_ Size>Set_Image_Print_Resolution.

(tutorial written according to this link)
9 Comments

Create an Impactful Scientific Poster

2/19/2014

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Thousands of posters are presented ever year at conferences and meetings across the world. How can you make your poster stand out?

Take 3 minutes to learn how to clearly display your work in this ACS Webinet.  



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2012 Structure-Based Drug Design Conference presentations free online

2/26/2013

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You can download complimentary speaker presentations from the CHI's 2012 Structure-Based Drug Design (SBDD) conference by simply filling in a registration form here:

Making Docking/Scoring Calculations More Accurate via Error Analysis

Authored by: Kenneth M. Merz, Jr., Ph.D., Department of Chemistry, Quantum Theory Project, University of Florida
  • Challenges facing computational biology
  • Water models and water dimer
  • 2010 GPCR docking and modeling competition
  • What about the docking funnel?
Download Presentation 
 
Rational Approaches to Improving Selectivity in Drug Design
Authored by: Woody Sherman, Ph.D., Vice President, Applications Science, Shrodinger
  • Factors contributing to selectivity 
  • Shape complementarity: Clash with decoy  
    • Remove decoy interactions
  • Induced fit of target
  • Experimental validation
Download Presentation
 
Structure based Ligand Discovery for GPCRs

Authored by: Ruben Abagyan, Ph.D., Professor, Skaggs School of Pharmacy & Pharmaceutical Sciences, San Diego Supercomputer Center, University of California, San Diego
  • Growing understanding of GPCR structure and function
  • Docking to flexible sites: methods and benchmarks
  • 2010 GPCR docking and modeling competition
  • Ligand guided modeling of unsolved GPCRs and alternative states
Download Presentation  

Making Decisions in Fragment-Based Drug Discovery
Authored by: Rod Hubbard, Ph.D., Director, Structural Sciences, Vernalis Ltd.
  • Overview of fragment-based methods
    • Some (old) examples of successes
  • Some fragmentology
    • Hit rates and target druggability
    • Predicting fragment poses
    • Selectivity
      How to make decisions on which fragments to progress?
  • What are the opportunities for computational methods?
Download Presentation

This is the agenda for the 2013 Structure-Based Drug Design Conference.

Zoe

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Protein and molecule rendering in Matlab 

11/7/2012

2 Comments

 
In this link you can find details about rendering proteins or molecules with Matlab.
Evi

2 Comments

Creating a high quality image with VMD

10/1/2012

1 Comment

 
Here is a collection of VMD tutorials that Evi Gkeka has gathered in order to help you make high quality biomolecular images.

1. VISUALIZING MOLECULES WITH VMD

2. VMD - Exercises on High Resolution Graphics

3. VMD Tutorial (by Evi Gkeka)


Also, the VMD site has a collection of scripts organized in a library that you may find useful.

Zoe
1 Comment

How to deliver amazing, motivational presentations

5/4/2012

0 Comments

 
All of these tips are excellent and absolutely needed for mastering presentations. Some of the tips are adapted from this article.

1. Do You have a Special Message to Deliver?
Remember that you are giving this talk because you have a special message to deliver to the audience. You should determine the specifics that you want to get across. What does your audience want to hear and can you deliver that kind of message? Being too general or vague will simply minimize your chances of success before you have even gotten started. Work through that message and try to create a story around it. People love stories! And remember to repeat the message that you want to get across a few times! Not just once!

2. You May Need a Mentor
Sometimes you get too sucked in in your own presenation that you might miss the bigger picture. Having a mentor or colleague to show your slides a few days before your talk is a great idea. Most of the times you get excellent feedback that you can use. Also, see what others are doing. Establish connections. Having a mentor will help you refine your skills.

3. The Target Audience
Know what your target audience is before you start writing your presentation. Each group of people will have to be approached in a specific way. If you have no idea who will be receiving your speeches, you will fail making those highly specific and relevant.

4. Work on Your Public Speaking Skills
Even if you have the best personal stories and lessons to share, you will fail due to poor speaking skills. Work hard on mastering your public speaking. The best way to see what you are doing is to videotape your speeches. Once you do it, watch the records very carefully. Pay attention to your intonation, your body languages and the eye contact you establish with the audience (this is very important!). Learn how to sound natural and reassuring. If you need to, enroll in a public speaking course that will help you polish your skills.

5. Be enthusiastic
I cannot stress enough the value of being enthusiastic. If you are not enthusiastic about your results and presentation, don't expect others to be enthusiastic. Remember: you are presenting unique results that you have worked hard for! There is a special message to deliver and you are the first person to ever pass this message across!

6. Understand Your Audience’s Feedback
Good presenters listen to their audience. Learn how to ask for feedback and how to listen to the things that people have to say. The easiest way to receive some information is through the creation of a simple poll. Be ready to modify anything that seems to be failing. Also, be enthusiastic about your feedback, NOT angry or disappointed! People have taken the time to listen to you and want to help you improve the weak points so that next time you will be better and better.

7. A Good Speaker is a Good Writer
Publish articles and informative pieces in blogs, websites and specialized magazines. Apart from being a good form of publicity, it will help you master your motivational speaking skills. A good speaker is a good writer, as well. Learn how to master both.

8. Be Flexible!
The most important rule for any professional is to maintain a degree of flexibility. Be ready to change parts of your speech at any time. Do not become emotionally attached to your talk as the things you considered successful may fail influencing your audience. Next time, try a different approach.

9. Know your stuff
Make sure you know what EVERY SINGLE WORD on your slides mean as well as the principle behind each central concept that you are using (i.e. what is the principle behind minimization or molecular dynamics?). Remember, you are on the spot up there and never know what people may ask you.

9. Acknowledge
It is ABSOLUTELY NECESSARY to include an acknowledgement slide at the end of your presentation no matter how formal or informal your seminar is. Who provided you with data? Who helped you with your research or by discussing critical aspects of the project? Who are your collaborators?


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    Alexis, Maria, Dimitra, Ioannis,  Michalis, Danai, Panos, George, Aspa, Zoe

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