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Joined: 11/14/2017
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I can´t see the protein or the ED. Centering with "Q" doesn´t change anything.
What can I do?

> Puzzle 1606 - ED

jeff101's picture
User offline. Last seen 1 day 3 hours ago. Offline
Joined: 04/20/2012
Groups: Go Science
Try the Home key & the ED Menu.
To see the protein, you should try the Home key.

To see the ED Cloud in the Original Interface, look 
under Actions for Electron Density, then click on 
it to bring up the Electron Density Menu. Then in 
the ED Menu, select something besides "None". Then 
click "Focus on Density" to center the ED Cloud on 
the screen. You might need to play with the Alpha & 
Threshold sliders to see the ED Cloud. One combination 
that should work is "Solid" with no check in the "Enable 
Backface Culling" box, the Red Green & Blue sliders over 
"add", and the Alpha & Threshold sliders over "r de".

Once you find the ED Cloud, you can click on the ED Menu's 
"Center Protein on Density" button to bring the protein 
into the ED Cloud (Warning: your score may drop).

Does that help?
Joined: 09/24/2012
Groups: Go Science
To see the protein

Home key is the key. But it's not always sufficient (e.g. for symmetric chains, "home" being in the middle of the 2 chains that can remain out of screen).

If "home" only shows you the protein, not the cloud (even after you've followed what Jeff101 explained) and in any case, you can do the following.

Move the protein very far from you, using the mouse middle ring or shift+drag&drop the background up. From far away, you'll localize everything (chains, clouds ...).

Centering with "q" only works with mouse on a segment (it will center to that segment). This is useful for symmetric or ED work.

Joined: 11/14/2017
Groups: None
Distance between protein and Electron Density

Thanks for your answers! Unfortunately, I´m too late to try to solve the problem again. Next time...?!

@jeff 101:
I´ve tried some of the functions with the ED Menu before, which you explained - without success.
Next time I´ll try again.

@Bruno Kestemont:
I´ve tried to move the protein with shift+drag&drop an strg+drag&drop before, too - without success.

Could it be possible, that the protein was in the very front (very near), so that I couldn´t see it? Or very, very far away?

In other ED puzzles I had had the problem, that the distance between the protein and the ED was too big, so that it was very difficult to see them both or move them together.

For me, centering the protein in ED often seemed to be not the suitable function because details in folding the protein will not be included (so far I understand). Therefore, sometimes the centered position was totaly in contrast to the intended position. Then it was difficult to keep the overview about the intended movements, foldings.

I would prefere to have a function to bring the protein "next to" the ED, so that both are visible in a short distance.
Perhaps a kind of "map" would help, too, to see the location of the protein and ED? And the possibility to move them together (like in the Rama Map)??

Sorry, English is not my favourite. And I´m not an expert!

Joined: 05/19/2017
Groups: None
Made a quick video response!

Hey Knoblerine!

I recorded something quick and dirty to help aid you, hopefully this should come in handy before the next ED puzzle. Have a watch. https://youtu.be/JwTWp5EG8YA

Joined: 11/14/2017
Groups: None
Electron Density Puzzles


these functions were important for me:

„Home key“ is the „Pos 1“ key! „Home key“ brought the protein in my sight again.
Even if the protein is too far away or very near and out of sight (with Shift + drag&drop is this possible!), with „Home key“/“Pos 1“ it´ll come in sight again.

Basic Electron Density Tutorial:
> I´ve learned how to recall expired puzzles and work on them; without scoring.
> Advanced GUI: There are some interesting functions. For me, it was very useful to see how I can move small parts of the protein.
I´ll need some training.
> The Electron Density Menue is important to get the best view of the structure of the Electron Density and to position the protein right in there. Trying the sliders will help to understand the functions.
> Changing the background colour from white to black or choosing different protein colourings are examples for further nice functions in Advanced GUI.

Thank you all! [Merry Xmas!]


Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons