[Jalview-discuss] Hydrophobicity and similar values

Mungo Carstairs (Staff) g.m.carstairs at dundee.ac.uk
Wed Jan 6 12:04:20 GMT 2016

Hello Celia,

The short answer is no -  Jalview does not compute values for these properties, so has no data that could be averaged over the structure for them.

Jalview does have built-in sequence colour schemes for hydrophobicity, helix propensity, and buried index (see http://www.jalview.org/help/html/colourSchemes/index.html), but these are based only on the amino acid residues (a global average), not on their context in the specific structure.

Dedicated structure viewers (Jalview supports integration with Chimera and Jmol) may have some capability to provide what you are after, but I will have to leave that to others more expert in those tools to comment on [&#X1f609] .

Best regards,


Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.

From: jalview-discuss-bounces at jalview.org <jalview-discuss-bounces at jalview.org> on behalf of Kun Rodrigues, Celia <celia.rodrigues at ucl.ac.uk>
Sent: 05 January 2016 16:36
To: jalview-discuss at jalview.org
Subject: [Jalview-discuss] Hydrophobicity and similar values

Dear Jalview Administrator,

If, given a pdb file, could Jalview give me average values of hydrophobicity, polarity, maybe propensity to be buried or to form helix, or maybe even surface or active centre accessibility for the whole protein structure? I just want one value for the whole structure.

Thank you,


The University of Dundee is a registered Scottish Charity, No: SC015096
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20160106/02df0192/attachment.html 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: OutlookEmoji-&amp;#X1f609.png
Type: image/png
Size: 390 bytes
Desc: OutlookEmoji-&amp;#X1f609.png
Url : http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20160106/02df0192/attachment.png 

More information about the Jalview-discuss mailing list