Re: [Jmol-users] Connecting atoms according to the sums of their atom/ionic radii ?
That looks good Bob. I understand that if the atoms are charged according to the CIF file, Jmol will use percentage bounds of the sum of the pairs of ionic radii, either those hard coded into Jmol or those input according to your previous extension. If the atoms are not charged, the bonding radius as defined by Jmol will be used in default. Thanks again for a rapid solution, as usual :-) Alan. Robert Hanson said: Got it! Turned out to be a very simple addition to the code. connect 80% 120% . The percent means combined nominal bonding radius If the atoms are charged, this is the ionic radius, possibly defined by the user. If the atoms are uncharged, this is the covalent/ionic radius that depends upon charge and is predefined by Jmol. So you can set this for the minimum or the maximum. Jmol 11.9.32 will also read -0.80 as 80% in this context, but I think 80% is a clearer syntax and will be the suggested method. see http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip Bob On Sun, Feb 28, 2010 at 5:39 PM, Alan Hewat he...@ill.fr wrote: Whether bonds connecting atoms are drawn or not should depend on the sum of the atom or ionic radii, and should not have to be specified as a distance for each atom pair. For example, instead of connecting atom sets within a range of distances in Angstroms eg: connect (~cations) (~anions) 0.8 2.5; it would be good to be able to connect them within a range of fractions of their combined ionic or atomic radii eg: connect (~cations) (~anions) 0.8 1.2 ionic; or connect (~cations) (~anions) 0.8 1.2 atomic; Alan __ Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE alan.he...@neutronoptics.com +33.476.98.41.68 http://www.NeutronOptics.com/hewat __ -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Connecting atoms according to the sums of their atom/ionic radii ?
Right. If the user has specified
{xxx}.ionic = .
then those values will be used.
On Thu, Mar 4, 2010 at 10:33 AM, Alan Hewat he...@ill.fr wrote:
That looks good Bob. I understand that if the atoms are charged according
to the CIF file, Jmol will use percentage bounds of the sum of the pairs
of ionic radii, either those hard coded into Jmol or those input according
to your previous extension. If the atoms are not charged, the bonding
radius as defined by Jmol will be used in default.
Thanks again for a rapid solution, as usual :-) Alan.
Robert Hanson said:
Got it! Turned out to be a very simple addition to the code.
connect 80% 120% .
The percent means combined nominal bonding radius
If the atoms are charged, this is the ionic radius, possibly defined by
the user. If the atoms are uncharged, this is the covalent/ionic radius
that depends upon charge and is predefined by Jmol.
So you can set this for the minimum or the maximum. Jmol 11.9.32 will
also
read -0.80 as 80% in this context, but I think 80% is a clearer
syntax and will be the suggested method.
see http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
Bob
On Sun, Feb 28, 2010 at 5:39 PM, Alan Hewat he...@ill.fr wrote:
Whether bonds connecting atoms are drawn or not should depend on the sum
of the atom or ionic radii, and should not have to be specified as a
distance for each atom pair. For example, instead of connecting atom
sets within a range of distances in Angstroms eg:
connect (~cations) (~anions) 0.8 2.5;
it would be good to be able to connect them within a range of fractions
of their combined ionic or atomic radii eg:
connect (~cations) (~anions) 0.8 1.2 ionic;
or
connect (~cations) (~anions) 0.8 1.2 atomic;
Alan
__
Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE
alan.he...@neutronoptics.com +33.476.98.41.68
http://www.NeutronOptics.com/hewat
__
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
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
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Mac Question re unbind/bind
Hello,
I'm using the following start up script to unbind and bind CTRL operations:
unbind 'CTRL-LEFT'; bind 'CTRL-LEFT' 'rotateSelected Y
_DELTAX;rotateSelected X _DELTAY;';unbind 'CTRL-RIGHT'; bind 'CTRL-RIGHT'
'translateSelected {_DELTAX/100 _DELTAY/-100 0};'
Under Windows, the script works with Firefox, MSIE, and Chrome. Under Mac
(Firefox and Safari), I am getting user reports that the translation works,
but the rotation does not. Specifically, the unbind of CTRL-LEFT seems to
work, but the bound script does not work. The assessment that the unbind is
working is based on the fact that CTRL-LEFT does nothing. It should, I
think, raise the Jmol menu, so it seems to be properly disconnected by the
above script.
Three questions:
1. Does anyone see a problem with my rotation script? I should note that the
rotateSelected Y _DELTAX format is intentional.
2. Is there anything special about CTRL-LEFT on a Mac that might interfere
with this?
3. I don't have convenient access to a Mac, can anyone easily swap LEFT and
RIGHT in the above script to check if the swap moves the problem to the
translate and fixes the rotate? The following page has a command field that
could check this:
http://chemagic.com/web_molecules/script_page_large.aspx
Otis
--
Otis Rothenberger
http://chemagic.org
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MSIE and Jmol bind
where's the page?
On Tue, Mar 2, 2010 at 11:50 PM, Otis Rothenberger o...@chemagic.comwrote:
Bob,
Here is what's not working for me:
jmolApplet(450, load /models/alkane!ethane_mm.mol;moveto 0 1 1 1 66;hover
off;frank off;set PickCallBack 'processPick';javascript appletLoadedA(),
01)
MSIE picks up everything but the last javascript call. I've tried
appletLoadedA()
with and without quotes. Chrome and Firefox get it, MSIE does not.
I have a command text field that runs Jmol script and JavaScript. If I send
appletLoadedA() via the javascript route in this field, MSIE gets it, and
the bind works. If I send it via the Jmol script route, MSIE does not seem
to get it. It's almost as if Jmol script javascript is not working at all on
MSIE.
Otis
On Tue, Mar 2, 2010 at 11:25 PM, Robert Hanson hans...@stolaf.edu wrote:
That makes no sense. None of this bind/unbind stuff is browser dependent.
What could this be? Could be that CTRL-LEFT doesn't work in MSIE 8, period
-- bound or unbound. Maybe MSIE 8 uses CTRL-LEFT for something else and
doesn't pass it on the the applet. It should call up the menu.
On Tue, Mar 2, 2010 at 8:49 PM, Otis Rothenberger o...@chemagic.comwrote:
Hello-
I'm using the bind command on Jmol 11.9.30_dev to set up mouse rotation
and translation of individual molecular models or molecular fragments in a
window. The fragments are in the same frame, and they are click pick
selected for rotation/translation action.
The following script is run via an applet loaded function at start-up.
jmolScript(frank on;unbind 'CTRL-LEFT'; bind 'CTRL-LEFT' 'rotateSelected
Y _DELTAX;rotateSelected X _DELTAY;';unbind 'CTRL-RIGHT'; bind 'CTRL-RIGHT'
'translateSelected {_DELTAX/100 _DELTAY/-100 0};', 01);
On XP, the subsequent mouse rotations and translations work fine on
Firefox and Chrome, but MSIE 8.0.6... does not bind or unbind. In MSIE,
the fragment selections are working, but the mouse bindings stay on the Jmol
defaults.
Does anyone know if there is a MSIE tweak for bind and unbind or is
this simply a case of it does not work on MSIE? I don't have any Mac
information on this at this point.
Otis
--
Otis Rothenberger
http://chemagic.org
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
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
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Otis Rothenberger
http://chemagic.org
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
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
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac Question re unbind/bind
Bob-
Very interested! Thanks.
How about translate?
Otis
On Thu, Mar 4, 2010 at 1:53 PM, Robert Hanson hans...@stolaf.edu wrote:
Otis, in case you are interested, here is what Jmol does with the standard
mouse click motion, in this order though not using exactly this command:
rotate X @{180.0 * _deltaY / _Height * mouseDragFactor};
rotate Y @{180.0 * _deltaX / _Width * mouseDragFactor};
But, right, there must be something about CTRL-LEFT and the Mac.
Bob
On Thu, Mar 4, 2010 at 12:30 PM, Otis Rothenberger o...@chemagic.comwrote:
Hello,
I'm using the following start up script to unbind and bind CTRL
operations:
unbind 'CTRL-LEFT'; bind 'CTRL-LEFT' 'rotateSelected Y
_DELTAX;rotateSelected X _DELTAY;';unbind 'CTRL-RIGHT'; bind 'CTRL-RIGHT'
'translateSelected {_DELTAX/100 _DELTAY/-100 0};'
Under Windows, the script works with Firefox, MSIE, and Chrome. Under Mac
(Firefox and Safari), I am getting user reports that the translation works,
but the rotation does not. Specifically, the unbind of CTRL-LEFT seems to
work, but the bound script does not work. The assessment that the unbind is
working is based on the fact that CTRL-LEFT does nothing. It should, I
think, raise the Jmol menu, so it seems to be properly disconnected by the
above script.
Three questions:
1. Does anyone see a problem with my rotation script? I should note that
the rotateSelected Y _DELTAX format is intentional.
2. Is there anything special about CTRL-LEFT on a Mac that might interfere
with this?
3. I don't have convenient access to a Mac, can anyone easily swap LEFT
and RIGHT in the above script to check if the swap moves the problem to the
translate and fixes the rotate? The following page has a command field that
could check this:
http://chemagic.com/web_molecules/script_page_large.aspx
Otis
--
Otis Rothenberger
http://chemagic.org
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
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
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Otis Rothenberger
http://chemagic.org
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MSIE and Jmol bind
Bob,
I moved the bind/unbind directly into the Jmol load script. The only thing
the javascript function does now is enter some field information after the
applet loads, at least that's the intent. Moving the bind/unbind directly
into the script solved the bind/unbind problem in MSIE, but MSIE is not
getting the javascript. The page is our virtual model kit that involved
exploring Jmol editor features. The goal here was not so much building
molecules, but rather manipulating them the same way freshman and sophomore
students manipulate Prentice/Hall models during a models lab. Nevertheless,
it turns out the build feature is an important component. The URL:
http://chemagic.com/web_molecules/script_page_large.aspx
My friend at USM is working on instruction docs, but the Molecular Editor
link leads to some page instructions.
Otis
On Thu, Mar 4, 2010 at 1:59 PM, Robert Hanson hans...@stolaf.edu wrote:
where's the page?
On Tue, Mar 2, 2010 at 11:50 PM, Otis Rothenberger o...@chemagic.comwrote:
Bob,
Here is what's not working for me:
jmolApplet(450, load /models/alkane!ethane_mm.mol;moveto 0 1 1 1
66;hover off;frank off;set PickCallBack 'processPick';javascript
appletLoadedA(), 01)
MSIE picks up everything but the last javascript call. I've tried
appletLoadedA()
with and without quotes. Chrome and Firefox get it, MSIE does not.
I have a command text field that runs Jmol script and JavaScript. If I
send appletLoadedA() via the javascript route in this field, MSIE gets
it, and the bind works. If I send it via the Jmol script route, MSIE does
not seem to get it. It's almost as if Jmol script javascript is not working
at all on MSIE.
Otis
On Tue, Mar 2, 2010 at 11:25 PM, Robert Hanson hans...@stolaf.eduwrote:
That makes no sense. None of this bind/unbind stuff is browser dependent.
What could this be? Could be that CTRL-LEFT doesn't work in MSIE 8, period
-- bound or unbound. Maybe MSIE 8 uses CTRL-LEFT for something else and
doesn't pass it on the the applet. It should call up the menu.
On Tue, Mar 2, 2010 at 8:49 PM, Otis Rothenberger o...@chemagic.comwrote:
Hello-
I'm using the bind command on Jmol 11.9.30_dev to set up mouse
rotation and translation of individual molecular models or molecular
fragments in a window. The fragments are in the same frame, and they are
click pick selected for rotation/translation action.
The following script is run via an applet loaded function at start-up.
jmolScript(frank on;unbind 'CTRL-LEFT'; bind 'CTRL-LEFT'
'rotateSelected Y _DELTAX;rotateSelected X _DELTAY;';unbind 'CTRL-RIGHT';
bind 'CTRL-RIGHT' 'translateSelected {_DELTAX/100 _DELTAY/-100 0};',
01);
On XP, the subsequent mouse rotations and translations work fine on
Firefox and Chrome, but MSIE 8.0.6... does not bind or unbind. In
MSIE,
the fragment selections are working, but the mouse bindings stay on the
Jmol
defaults.
Does anyone know if there is a MSIE tweak for bind and unbind or is
this simply a case of it does not work on MSIE? I don't have any Mac
information on this at this point.
Otis
--
Otis Rothenberger
http://chemagic.org
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
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
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Otis Rothenberger
http://chemagic.org
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Jmol-users mailing list
Re: [Jmol-users] MSIE and Jmol bind
ignore
When I go to your page and execute
javascript:alert(
appletLoadedA)
That reports a function with Firefox but no function with MSIE. Is that
what you observe as well?
So something in your code is not working.
/ignore
second part is what I wanted to say.
On Thu, Mar 4, 2010 at 2:40 PM, Robert Hanson hans...@stolaf.edu wrote:
Otis, there's something wrong with your JavaScript. MSIE 8.0.7100.0 on my
Windows7 machine works fine with a simple test. The page is simply
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
If you get an alert test when the page loads, that's Jmol sending
javascript back. It worked fine for me.
What I see from the Java console is that when Jmol executes in JAVASCRIPT
the command
!!_jmol.noEval
and needs to get a TRUE back from that, it instead gets a null pointer
error from the browser.
So it's something very specific to your page. I can't pinpoint what it is,
but the same sort of code is being executed on my page, and it works just
fine.
Bob
Bob
On Thu, Mar 4, 2010 at 1:20 PM, Otis Rothenberger o...@chemagic.comwrote:
Bob,
I moved the bind/unbind directly into the Jmol load script. The only thing
the javascript function does now is enter some field information after the
applet loads, at least that's the intent. Moving the bind/unbind directly
into the script solved the bind/unbind problem in MSIE, but MSIE is not
getting the javascript. The page is our virtual model kit that involved
exploring Jmol editor features. The goal here was not so much building
molecules, but rather manipulating them the same way freshman and sophomore
students manipulate Prentice/Hall models during a models lab. Nevertheless,
it turns out the build feature is an important component. The URL:
http://chemagic.com/web_molecules/script_page_large.aspx
My friend at USM is working on instruction docs, but the Molecular Editor
link leads to some page instructions.
Otis
On Thu, Mar 4, 2010 at 1:59 PM, Robert Hanson hans...@stolaf.edu wrote:
where's the page?
On Tue, Mar 2, 2010 at 11:50 PM, Otis Rothenberger o...@chemagic.comwrote:
Bob,
Here is what's not working for me:
jmolApplet(450, load /models/alkane!ethane_mm.mol;moveto 0 1 1 1
66;hover off;frank off;set PickCallBack 'processPick';javascript
appletLoadedA(), 01)
MSIE picks up everything but the last javascript call. I've tried
appletLoadedA()
with and without quotes. Chrome and Firefox get it, MSIE does not.
I have a command text field that runs Jmol script and JavaScript. If I
send appletLoadedA() via the javascript route in this field, MSIE gets
it, and the bind works. If I send it via the Jmol script route, MSIE
does not seem to get it. It's almost as if Jmol script javascript is not
working at all on MSIE.
Otis
On Tue, Mar 2, 2010 at 11:25 PM, Robert Hanson hans...@stolaf.eduwrote:
That makes no sense. None of this bind/unbind stuff is browser
dependent. What could this be? Could be that CTRL-LEFT doesn't work in
MSIE
8, period -- bound or unbound. Maybe MSIE 8 uses CTRL-LEFT for something
else and doesn't pass it on the the applet. It should call up the menu.
On Tue, Mar 2, 2010 at 8:49 PM, Otis Rothenberger
o...@chemagic.comwrote:
Hello-
I'm using the bind command on Jmol 11.9.30_dev to set up mouse
rotation and translation of individual molecular models or molecular
fragments in a window. The fragments are in the same frame, and they are
click pick selected for rotation/translation action.
The following script is run via an applet loaded function at start-up.
jmolScript(frank on;unbind 'CTRL-LEFT'; bind 'CTRL-LEFT'
'rotateSelected Y _DELTAX;rotateSelected X _DELTAY;';unbind 'CTRL-RIGHT';
bind 'CTRL-RIGHT' 'translateSelected {_DELTAX/100 _DELTAY/-100 0};',
01);
On XP, the subsequent mouse rotations and translations work fine on
Firefox and Chrome, but MSIE 8.0.6... does not bind or unbind. In
MSIE,
the fragment selections are working, but the mouse bindings stay on the
Jmol
defaults.
Does anyone know if there is a MSIE tweak for bind and unbind or
is this simply a case of it does not work on MSIE? I don't have any Mac
information on this at this point.
Otis
--
Otis Rothenberger
http://chemagic.org
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
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
[Jmol-users] problem with H-bonds -- a bug?
I am working on a student exercise on lysozyme, file 2LYZ, in which I want the students to see the locations of the helices and sheets in the overall structure. To get a view of the beta sheet with clearly visibile H-bonds, I type wireframe 100;spacefill off restrict sheet; hbonds calculate; hbonds 40 Then to show where this is located in the molecule I type select not sheet; wireframe Now I want to do something similar with one of the helices. I type select 5-14 and immediately the H-bonds in the sheet shrink to the narrow default wireframe width. Typing select sheet;hbonds 40 will not restore them. When I type select 5-14; hbonds calculate; hbonds 40 I see only the narrow H-bonds, and I have no control over their width any more. Does anyone know why this is happening and how to get around it? Jeff Cohlberg -- Jeffrey A. Cohlberg, Professor and Chair Department of Chemistry and Biochemistry California State University, Long Beach Long Beach, CA 90840 562-985-4944 fax 775-248-1263 cohlb...@csulb.edu -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac Question re unbind/bind
Otis,
This issue may be that the system binds cntrl-left = right mouse
button. This is because until recently most macs came with a one
button mouse. I always replaced it with a two-button/scroll-wheel
mouse:). But on my mice the cntl-left still brings up the context
sensitive right button menus. My guess is your unbind is only
affecting the browser, so everything is captured by the OS and you
don't get signal passed through.
Jonathan
On Mar 4, 2010, at 1:05 PM, jmol-users-requ...@lists.sourceforge.net
wrote:
Message: 3
Date: Thu, 4 Mar 2010 13:30:44 -0500
From: Otis Rothenberger o...@chemagic.com
Subject: [Jmol-users] Mac Question re unbind/bind
To: jmol-users@lists.sourceforge.net
Message-ID:
daf3612f1003041030y703525ady7cbc7981a1bf8...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1
Hello,
I'm using the following start up script to unbind and bind CTRL
operations:
unbind 'CTRL-LEFT'; bind 'CTRL-LEFT' 'rotateSelected Y
_DELTAX;rotateSelected X _DELTAY;';unbind 'CTRL-RIGHT'; bind 'CTRL-
RIGHT'
'translateSelected {_DELTAX/100 _DELTAY/-100 0};'
Under Windows, the script works with Firefox, MSIE, and Chrome.
Under Mac
(Firefox and Safari), I am getting user reports that the translation
works,
but the rotation does not. Specifically, the unbind of CTRL-LEFT
seems to
work, but the bound script does not work. The assessment that the
unbind is
working is based on the fact that CTRL-LEFT does nothing. It should, I
think, raise the Jmol menu, so it seems to be properly disconnected
by the
above script.
Three questions:
1. Does anyone see a problem with my rotation script? I should note
that the
rotateSelected Y _DELTAX format is intentional.
2. Is there anything special about CTRL-LEFT on a Mac that might
interfere
with this?
3. I don't have convenient access to a Mac, can anyone easily swap
LEFT and
RIGHT in the above script to check if the swap moves the problem to
the
translate and fixes the rotate? The following page has a command
field that
could check this:
http://chemagic.com/web_molecules/script_page_large.aspx
Otis
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
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
