Question: How do I download and install DSSP?
0
gravatar for westin.kosater
10 weeks ago by
westin.kosater0 wrote:

I am looking through the Biopython Tutorial and Cookbook (http://biopython.org/DIST/docs/tutorial/Tutorial.html) and in order to look at DSSP files with biopython, I need to obtain a copy and license of DSSP from this link (https://swift.cmbi.umcn.nl/gv/dssp/). Could somebody please explain how I take the files from github and install them to my computer? I downloaded the files on my computer and put them in my current working directory in python and I'm still not able to use DSSP files in biopython

dssp biopython python • 235 views
ADD COMMENTlink modified 10 weeks ago by jrj.healey9.9k • written 10 weeks ago by westin.kosater0
2
gravatar for jrj.healey
10 weeks ago by
jrj.healey9.9k
United Kingdom
jrj.healey9.9k wrote:

I'd suggest using conda to install it:

conda install -c salilab dssp

So long as you have the dssp* binary available in your $PATH, BioPython should be happy.

*It may be called mkdssp

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by jrj.healey9.9k

Thank you. As a follow up question., how can I make sure that the dssp binary is in $PATH?

ADD REPLYlink written 10 weeks ago by westin.kosater0

If you went through conda, it should take care of that for you.

You can test it by running:

which dssp or which mkdssp.

One of those should print you a file path. On my machine for example, I get this:

$ which mkdssp
/home/wms_joe/bin/miniconda2/bin/mkdssp

That should be sufficient for BioPython.

which is not always available on all OSs, so you can also use type. In any event, you should see its install path printed out. If you dont, this means it is not in the $PATH *or conda itself isn't configured correctly, but come back to us if that's the case.

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by jrj.healey9.9k
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