Re: [Jmol-users] try your hand at stereochemistry
On Fri, Oct 14, 2011 at 1:02 AM, Robert Hanson wrote: > http://chemapps.stolaf.edu/jmol/docs/examples-12/isomers.htm What's up with example 4? The MFs don't match... or is that intentional? > Just thought of this idea -- will be developing the page to have more > examples. Note that under the applets it shows what commands were given. I suggest adding some examples from the CIP papers :) Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet (http://ki.se/imm) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- 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-d2d-oct ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rendering in POV-Ray broken in 12.2.0
works fine for me in 12.2.1 and 12.2.0. Maybe it's some other problem on your machine? 2011/10/13 Sérgio Ceroni da Silva > Works fine in 12.0.49 > > > -- > 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-d2d-oct > ___ > 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-d2d-oct___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Rendering in POV-Ray broken in 12.2.0
Works fine in 12.0.49 -- 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-d2d-oct ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] try your hand at stereochemistry
http://chemapps.stolaf.edu/jmol/docs/examples-12/isomers.htm Just thought of this idea -- will be developing the page to have more examples. Note that under the applets it shows what commands were given. -- 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-d2d-oct___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] select atoms displayed as wireframe/cartoon/vdw
Hi,
lol, I just found out about some nice atom properties while I was about to
suggest a feature...
{}.backbone
{}.cartoon
{}.cpk
{}.meshribbon
{}.radius
{}.ribbon
{}.rocket
{}.spacefill
{}.trace
You can use these in select statements as well as to set the style!
Afaik these are not documented (I hope there are here to stay though), but you
can find them via '{}.?'. An option for the wireframe style is missing here as
it is not the property of a single atom. Maybe there is a hidden option in the
connect command or in the connected() function to select bonds by their width
(and thus change them selectively)?
Best
Alexander
- message draft
I am looking for a way to select all atoms currently displayed as
wireframe/cartoon/vdw (including width, radius). In other words, sort of a
local display style state as opposed to the global state of everything, because
that would reload everything and you would also loose any variables and
functions previously defined.
This would allow me to change the display style temporarily from A to B without
having to know what created A in the first place. Consider fo example the
following two use cases.
When you look at a ligand in a binding pocket it is nice to be able to switch
the wireframe of the surrounding residues on and off. So far so good - just do
it, create a button in your ligand-protein-viewing-web-app and you can switch
at lightning speed. But wait, now there is some special residue (of the
surrounding ones) I just found out about and I want to display in a special
way. I can do that but that special display style could be destroyed every time
I click the toggle button.
Some parts of a protein are displayed in the cartoon style and now you realize
the cartoon is too thick. You can change the thickness cartoon only if you know
what is display in the cartoon style.
--
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-d2d-oct
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Re: [Jmol-users] protein-ligand - viewing together in the same frame
El 13 Oct 2011 a las 11:45, Sam Paul D. escribió: > As a research scholar working in molecular docking,I felt why can't > this be done at the click of a button instead of writing the > script everytime? > Please suggest. Sam, write a webpage and insert the button there, using the Jmol.js library abilities If you use the signed applet you have full functionality like drag and drop your file into the applet. -- 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-d2d-oct ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] 'connect delete' also deletes measurements
Hi,
that is great, a real timesaver for me!
Alex
- Ursprüngliche Mail -
> Von: "Robert Hanson"
> An: jmol-users@lists.sourceforge.net
> Gesendet: Mittwoch, 12. Oktober 2011 16:15:24
> Betreff: Re: [Jmol-users] 'connect delete' also deletes measurements
> For some reason I thought that was important to do, but I certainly
> can't think of why. My note to self says it is because leaving the
> measurements in would mess up the state, but I can't imagine why that
> would be true. Maybe in a really early version of the state the
> connections were indicated differently. No atoms are removed, just
> connections. So I'll consider it a bug until someone tells me I have
> to put it back in.
>
> See http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
>
>
>
>
> On Wed, Oct 12, 2011 at 8:44 AM, Alexander Rose <
> alexander.r...@weirdbyte.de > wrote:
>
>
> Hi,
>
> on http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm with
> caffeine loaded
> try 'measure {atomNo=2} {atomNo=7}; connect (atomNo=12) (atomNo=20)
> delete;'.
>
> Annoyingly, the connect also deletes the measurement.
>
>
> Best
> Alexander
>
> --
> 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-d2d-oct
> ___
> 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-d2d-oct
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
--
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-d2d-oct
___
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