Re: [Jmol-users] MO display problem
actually it was not fixed -- just broken differently. I did just fix it now, though. RC6 in particular broke this. My VPN system went down during the file transfer, so we will have to wait for tomorrow, I think, for that update. On Wed, Apr 21, 2010 at 8:47 PM, Otis Rothenberger wrote: > OK, I see that this is fixed in RC7. I need to start checking updates > more frequently! > > Otis > > On 4/21/2010 7:29 PM, Otis Rothenberger wrote: > > Thanks Jonathan, > > > > Yes, I am using 12.0.RC6_dev. > > > > I did not know about the approach: > > > > isosurface modelmo mo 1 > > > > I can make what I want to do work with variations of this along with > labels. > > > > One other issue that I see is that some isosurface commands do not seem > > to work as before: > > > > isosurface mo 1 mesh nofill frontonly > > > > for example does not behave as expected. For the time being, your > > suggestion is a good one for me. > > > > > > Otis > > > > -- > Otis Rothenberger > chemagic.com > > > > > > -- > ___ > 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MO display problem
alas, I messed up isosurface and mo. I'm tracking it down... On Wed, Apr 21, 2010 at 5:48 PM, Jonathan Gutow wrote: > Verified on MacOS, Firefox 3.6.3 Java 1.5.0_22, you are using > Jmol12.0.RC6 (is that right). > > That is weird looking. I can also get it to happen when rotating by > hand. It looks as if the frame is changing, but it doesn't appear to > be. > > It does not appear to happen when the mo is created using the > isosurface command: > > isosurface modelmo mo 1 > > Jonathan > On Apr 21, 2010, at 1:50 PM, jmol-users-requ...@lists.sourceforge.net > wrote: > > > Message: 1 > > Date: Tue, 20 Apr 2010 12:35:35 -0400 > > From: Otis Rothenberger > > Subject: [Jmol-users] MO display problem > > To: Jmol Users > > Cc: Tom Newton > > Message-ID: <4bcdd7d7.2010...@chemagic.com> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > In Jmol 12.0.RC6_dev, I'm seeing peculiar behavior of MO's. Once > > displayed, the MO's disappear and reappear at various positions during > > mouse rotation or the spin command. > > > > The script > > > > load ../meps/alkene!1-butene_mo.mol;mo 1;spin > > > > in the script text field (followed by clicking Run) on the following > > page will illustrate the problem: > > > > http://chemagic.com/web_molecules/script_page_large.aspx > > > > Has anyone else seen this problem? I don't think it is related to > > other > > code on the page. > > > > Otis > > > > -- > > Otis Rothenberger > > Dr. Jonathan H. Gutow > Chemistry Department gu...@uwosh.edu > UW-Oshkosh Office:920-424-1326 > 800 Algoma Boulevard FAX:920-424-2042 > Oshkosh, WI 54901 > http://www.uwosh.edu/facstaff/gutow > > > > > > > > -- > ___ > 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MO display problem
OK, I see that this is fixed in RC7. I need to start checking updates more frequently! Otis On 4/21/2010 7:29 PM, Otis Rothenberger wrote: > Thanks Jonathan, > > Yes, I am using 12.0.RC6_dev. > > I did not know about the approach: > > isosurface modelmo mo 1 > > I can make what I want to do work with variations of this along with labels. > > One other issue that I see is that some isosurface commands do not seem > to work as before: > > isosurface mo 1 mesh nofill frontonly > > for example does not behave as expected. For the time being, your > suggestion is a good one for me. > > > Otis > -- Otis Rothenberger chemagic.com -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MO display problem
Thanks Jonathan, Yes, I am using 12.0.RC6_dev. I did not know about the approach: isosurface modelmo mo 1 I can make what I want to do work with variations of this along with labels. One other issue that I see is that some isosurface commands do not seem to work as before: isosurface mo 1 mesh nofill frontonly for example does not behave as expected. For the time being, your suggestion is a good one for me. Otis On 4/21/2010 6:48 PM, Jonathan Gutow wrote: > Verified on MacOS, Firefox 3.6.3 Java 1.5.0_22, you are using > Jmol12.0.RC6 (is that right). > > That is weird looking. I can also get it to happen when rotating by > hand. It looks as if the frame is changing, but it doesn't appear to > be. > > It does not appear to happen when the mo is created using the > isosurface command: > > isosurface modelmo mo 1 > > Jonathan > On Apr 21, 2010, at 1:50 PM, jmol-users-requ...@lists.sourceforge.net > wrote: > > > -- Otis Rothenberger chemagic.com -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MO display problem
Verified on MacOS, Firefox 3.6.3 Java 1.5.0_22, you are using Jmol12.0.RC6 (is that right). That is weird looking. I can also get it to happen when rotating by hand. It looks as if the frame is changing, but it doesn't appear to be. It does not appear to happen when the mo is created using the isosurface command: isosurface modelmo mo 1 Jonathan On Apr 21, 2010, at 1:50 PM, jmol-users-requ...@lists.sourceforge.net wrote: > Message: 1 > Date: Tue, 20 Apr 2010 12:35:35 -0400 > From: Otis Rothenberger > Subject: [Jmol-users] MO display problem > To: Jmol Users > Cc: Tom Newton > Message-ID: <4bcdd7d7.2010...@chemagic.com> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > In Jmol 12.0.RC6_dev, I'm seeing peculiar behavior of MO's. Once > displayed, the MO's disappear and reappear at various positions during > mouse rotation or the spin command. > > The script > > load ../meps/alkene!1-butene_mo.mol;mo 1;spin > > in the script text field (followed by clicking Run) on the following > page will illustrate the problem: > > http://chemagic.com/web_molecules/script_page_large.aspx > > Has anyone else seen this problem? I don't think it is related to > other > code on the page. > > Otis > > -- > Otis Rothenberger Dr. Jonathan H. Gutow Chemistry Department gu...@uwosh.edu UW-Oshkosh Office:920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] what is the reverse operation of jmolLoadInline?
Hello Francois-
The communication between the JME structure drawing applet and Jmol is
now very easy. In addition, Jmol will render these structures as 3D.
Consequently, the 3D molfile of a 2D structure can be created. Two way
communication is possible between JME and Jmol, but JME will render
returned information as 2D. One nice feature of this is that structures
can be exchanged by email as Web address query strings. We have an
operational system at:
http://chemagic.com/web_molecules/script_page_large.aspx
Click Display Molecular Editor, followed by the draw link.
JME is very light weight and very widely used.
Best Regards, Otis
On 4/21/2010 2:09 PM, Francois Nguyen wrote:
> Hi Angel.
>
> Thanks for the info. I have your book by the way!
>
> I am trying to make a web page with two applets: a jmol applet on one side
> and a Symyx Jdraw applet on the other and have them transfer the data back
> and forth.
>
> Extractmodel gives a MOL but it's not a CT file molfile. So Symyx Jdraw
> applet will not understand it.
>
> fileContents will give me the CT file if that's what I set originally; but if
> the data was set from an Xyz file, that's what I get back too, not a CT file.
>
> So it looks like jmol cannot be used as a converter between the various data
> formats.
> If rotations and translations will never affect the coordinates, as I always
> care about the whole structure, not a subset, I may be able to enforce
> starting from a CT-style Molfile.
>
>
> jmolGetPropertyAsString is simplest when in javascript:
>function getMolStringFromJmol()
>{
> return jmolGetPropertyAsString("fileContents");
>}
>
> -Francois
>
>
> -Original Message-
> From: Angel Herráez [mailto:angel.herr...@uah.es]
> Sent: Wednesday, April 21, 2010 1:19 AM
> To: jmol-users@lists.sourceforge.net
> Subject: Re: [Jmol-users] what is the reverse operation of jmolLoadInline?
>
> Hello, Francois
--
Otis Rothenberger
chemagic.com
--
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Re: [Jmol-users] Chime to Jmol
On Wed, Apr 21, 2010 at 8:42 PM, Robert Hanson wrote: > I know I'm not the first to think of doing this -- what else is out there in > this regard? There used to be a script to convert a Chime script into a Jmol script... have you used that? Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Chime to Jmol
I know -- aren't we done with Chime?? But I have added to http://chemapps.stolaf.edu/jmol/docs/examples-11/ the file ChimeToJmol.js This file, if along with Jmol.js is indicated in a SCRIPT tag in the HEAD section of a page that uses the Chime plug-in, should convert that page to Jmol. Will take some additional script conversion work to get this perfectly right -- anyone want to help? It would be nice to be able to say that you can take (just about) any Chime page and turn it instantly into a Jmol page. I know I'm not the first to think of doing this -- what else is out there in this regard? Bob -- 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] what is the reverse operation of jmolLoadInline?
Hi Angel.
Thanks for the info. I have your book by the way!
I am trying to make a web page with two applets: a jmol applet on one side and
a Symyx Jdraw applet on the other and have them transfer the data back and
forth.
Extractmodel gives a MOL but it's not a CT file molfile. So Symyx Jdraw applet
will not understand it.
fileContents will give me the CT file if that's what I set originally; but if
the data was set from an Xyz file, that's what I get back too, not a CT file.
So it looks like jmol cannot be used as a converter between the various data
formats.
If rotations and translations will never affect the coordinates, as I always
care about the whole structure, not a subset, I may be able to enforce starting
from a CT-style Molfile.
jmolGetPropertyAsString is simplest when in javascript:
function getMolStringFromJmol()
{
return jmolGetPropertyAsString("fileContents");
}
-Francois
-Original Message-
From: Angel Herráez [mailto:angel.herr...@uah.es]
Sent: Wednesday, April 21, 2010 1:19 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] what is the reverse operation of jmolLoadInline?
Hello, Francois
> However I can´t find the way to get the data back from jmol as a
> molfile.
This was commented a couple of days ago. Only for MOL format, you can
use
getProperty extractModel (atom expression)
(see http://chemapps.stolaf.edu/jmol/docs/)
For any format, there's also
getProperty fileContents
> I found how to get the data that was set, but if it is
> rotated for example, the atom coordinates will have changed.
No. The coordinates do not change as a consequence of model rotation
and translation.
> I think it may be something like jmolGetPropertyAsString
There's probably also a way to do it with that, but the above two
ones are simpler.
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Re: [Jmol-users] what is the reverse operation of jmolLoadInline?
Hello, Francois > However I can´t find the way to get the data back from jmol as a > molfile. This was commented a couple of days ago. Only for MOL format, you can use getProperty extractModel (atom expression) (see http://chemapps.stolaf.edu/jmol/docs/) For any format, there's also getProperty fileContents > I found how to get the data that was set, but if it is > rotated for example, the atom coordinates will have changed. No. The coordinates do not change as a consequence of model rotation and translation. > I think it may be something like jmolGetPropertyAsString There's probably also a way to do it with that, but the above two ones are simpler. -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
