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.

Bob Hanson

···

Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

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

Hello Bob,

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.

{1-40.*CA}

which would exclude any alternate locations (so I don’t match too many atoms).

My best effort so far is something like

{1.*CA[-1]|2.*CA[-1]|3.*CA[-1]…40.*CA[-1]}

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,

Mungo

The University of Dundee is a registered Scottish Charity, No: SC015096

···

Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
College of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk


From: jalview-dev-bounces@jalview.org jalview-dev-bounces@jalview.org on behalf of Robert Hanson hansonr@stolaf.edu
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.

Bob Hanson

Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

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

a bit off topic, but I am happy to oblige:

···

On Tue, Jun 2, 2015 at 11:12 AM, Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk> wrote:

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.

{1-40.*CA}

which would exclude any alternate locations (so I don’t match too many atoms).

As I am sure you know, alternate locations have special, not necessarily predictable, character codes. Generally there would be two or more alternate locations – something like A and B, or 1 and 2. So one would not usually remove all alt locs. The simple thing to do is use the CONFIGURATION command or select option:

select 1-40.ca and configuration=1

This selects for the first listed altloc, whatever it may be, along with altloc=""

Note that CONFIGURATION was broken some time before 2015.01.27 but fixed that day. So check your version if that does not work.

Bob

Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

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

Hey Bob,

···

On 03/06/2015 03:24, Robert Hanson wrote:

Note that CONFIGURATION was broken some time before 2015.01.27 but fixed that day. So check your version if that does not work.

That puts updating Jalview's version of Jmol to the top of the TODO list.

Jim.