I’m sure we all love a serious challenge, looking forward to it ;-).
By some weird synchronicity, I came across your name today while searching Jmol mailing list archives from 2006 on the topic of handling ‘alt location’.
I have a problem aligning structures in JMol (based on sequence alignment, and alpha carbons), whenever the CA atoms appear in alternate locations.
Essentially I need a variant of the selection pattern e.g.
which would exclude any alternate locations (so I don’t match too many atoms).
My best effort so far is something like
which seems to work but is unwieldy.
Does anything spring to mind how to address this? Or should I do the right thing and address the JMol mailing list?
Thanks and regards,
The University of Dundee is a registered Scottish Charity, No: SC015096
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
College of Life Sciences
University of Dundee, Dundee, Scotland, UK.
From: email@example.com firstname.lastname@example.org on behalf of Robert Hanson email@example.com
Sent: 02 June 2015 04:25
To: Jalview Development List
Subject: [Jalview-dev] Hello from Jmol
Thanks for adding me to this list. I am very excited to see if we can use Java2Script along with the Swing business I am working on now to do this. I am optimistic, though I realize it is a serious challenge.
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
If nature does not answer first what we want,
it is better to take what answer we get.
– Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900