FYI - see below about Java / Safari / latest OS/X
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Today’s Topics:
- Java in macOS High Sierra … is still available. (Rzepa, Henry S)
- Re: SMARTS question (Robert Hanson)
Message: 1
Date: Fri, 30 Jun 2017 12:30:06 +0000
From: “Rzepa, Henry S” h.rzepa@imperial.ac.uk
To: “jmol-users@lists.sourceforge.net”
jmol-users@lists.sourceforge.net
Cc: “Rzepa, Henry S” h.rzepa@imperial.ac.uk
Subject: [Jmol-users] Java in macOS High Sierra … is still
available.
Message-ID: A067DBAE-AE84-46C4-9EFC-CC84B05C7D65@imperial.ac.uk
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The public beta release allows testing of Java in this the latest version, presumed supported for a few years at least.
The Safari in this version is the same as the Safari Technology Preview.app which is available separately.
The relevant controls have moved to preferences/websites, where Java appears in the new plugins section. Java is off by default and has to be switched on. Any open website must then be selected to run with ?Run in safe mode? deselected (it is on by default). Once these are done, Jmol is again available, and read/write from a local file system is again enabled.
Of course Apple may decide to disable these (hidden) features are any stage, but at least they have made their way to their latest OS (with the caveat that this is still beta).
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Date: Fri, 30 Jun 2017 14:32:44 -0500
From: Robert Hanson hansonr@stolaf.edu
To: “jmol-users@lists.sourceforge.net”
jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] SMARTS question
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CAF_YUvUdXMk9k3RWbc+2Rskp5D=+4ch6B0o6JV+8iiUETME6oQ@mail.gmail.com
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make sure you have loaded the file with
set pdbAddHydrogens
SMARTS is really not designed to work with models that do not indicate
bonding.
You can also use Jmol BioSMARTS and target the sequences directly.
On Thu, Jun 29, 2017 at 12:28 PM, Eric Martz emartz@microbio.umass.edu wrote:
This selects the aromatic ring carbons of Phe and Tyr:
rings6 = {*}.find(“SMARTS”,“c1ccccc1”, true)
It does not select the 6-atom ring of Trp.
This selects the ring of His:
ringsh = {*}.find(“SMARTS”,“c1cncn1”, true)
How do I select the 5 and 6 atom rings of Trp?
Thanks, Eric
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–
Robert M. Hanson
Professor 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
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