http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
releasing official version this week.
On Mon, Oct 3, 2011 at 10:57 AM, Sara Bonner <bonn...@mit.edu> wrote:
> Hi
>
> The basic amino acids have a double bond but they are not shown by default
> in regular pdb files opened with Jmol's default settings. Ideally I would
> like to make the default settings for my work show double bonds when any pdb
> file is opened. It seems this is not an option so now I am trying to find a
> way to modify specific pdb files to specify where double bonds should be.
>
> For example see the definition of alanine on wikipedia which has a Jmol
> image of the amino acid
> http://chemapps.stolaf.edu/jmol/jmol.php?model=O%3DC%28O%29C%28N%29C
>
> The command set pdbAddHydrogens is not a known command in the current
> version of Jmol. I thought I read somewhere that this is in beta and will
> be release sometime in the near future.
>
> Thanks
> Sara
> ________________________________________
> From: Robert Hanson [hans...@stolaf.edu]
> Sent: Monday, October 03, 2011 11:36 AM
> To: jmol-users@lists.sourceforge.net
> Subject: Re: [Jmol-users] Double Bonds
>
> Before you get too excited about this, please try:
>
> set pdbAddHydrogens
> load "xxxx.pdb"
>
> Now, if this really is NOT a PDB file (which I guess that is not) consider
> reading the PDB LIGAND entry for fumarate instead.
>
> Why are you using PDB here, by the way?
>
>
>
> On Mon, Oct 3, 2011 at 10:00 AM, Sara Bonner <bonn...@mit.edu<mailto:
> bonn...@mit.edu>> wrote:
> HI Angel
>
> I didn't realize jmol scrip could be incorporated into a pdb! This is
> wonderful. I will give it a try.
>
> I've attached the format example for inserting double bonds using CONECT in
> a pdb. I was unable to see double bonds when I loaded this file or modified
> other files using this format.
>
> Thanks
> Sara
>
> ------------------------------------------------------------------------------
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>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
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