Comments on: Protein flexibility calculation with Python https://www.polarmicrobes.org/protein-flexibility-calculation-with-python/ Marine Microbial Ecology Thu, 11 Oct 2018 16:06:24 +0000 hourly 1 https://wordpress.org/?v=6.9.4 By: Jeff https://www.polarmicrobes.org/protein-flexibility-calculation-with-python/#comment-395 Thu, 11 Oct 2018 16:06:24 +0000 http://www.polarmicrobes.org/?p=1181#comment-395 In reply to Alexios Chatzigoulas.

Cool, thanks Alexios!

]]> By: Alexios Chatzigoulas https://www.polarmicrobes.org/protein-flexibility-calculation-with-python/#comment-394 Thu, 11 Oct 2018 15:31:13 +0000 http://www.polarmicrobes.org/?p=1181#comment-394 Very nice and helpful work. I have a few suggestions to make it even better. The way you smooth the b_factors searches the next 8 amino acids while it should look on the next 4 and the previous 4 amino acids. Also your if statement (if len(win) == 9) prevents the return of all values. I suggest the following code for the smoothing:

## average over 9 aa window
b_factors_win = []
it = 0
for b in range(0, len(b_factors)):
if b in range(0,4):
win = b_factors[b – it:b + 5]
b_win = sum(map(float, win)) / len(win)
b_factors_win.append(b_win)
it += 1
else:
win = b_factors[b – 4:b + 5]
b_win = sum(map(float, win)) / len(win)
b_factors_win.append(b_win)

]]> By: Jeff https://www.polarmicrobes.org/protein-flexibility-calculation-with-python/#comment-289 Thu, 10 Dec 2015 16:48:37 +0000 http://www.polarmicrobes.org/?p=1181#comment-289 In reply to Pedro Avellar Costa.

Thanks for inquiring… unfortunately we have not included this in a publication yet (on the to do list!). Feel free to use the code with a mention in acknowledgements.

]]> By: Pedro Avellar Costa https://www.polarmicrobes.org/protein-flexibility-calculation-with-python/#comment-288 Thu, 10 Dec 2015 14:48:02 +0000 http://www.polarmicrobes.org/?p=1181#comment-288 Any chance you have published anywhere so I can properly reference you?

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