Re: [Jmol-users] Errors upgrading to Jmol 11.6.13 from Jmol 11.5.51
I usually release the Jmol versions on sourceforge but I am currently out of town. I will probably be able to make the releases on sourceforge by the end of the week. Nico On Wed, Jan 21, 2009 at 7:23 AM, lspri...@weizmann.ac.il wrote: According to Robert Hanson hans...@stolaf.edu: I found both problems and have corrected them for Jmol 11.6.14 and Jmol 11.7.22. Bob Great. Can you please update the sourceforge.net download page or provide an alternative download URL? Thanks again, Jaim -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Errors upgrading to Jmol 11.6.13 from Jmol 11.5.51
Ok great! Thanks. Eran On Wed, Jan 21, 2009 at 11:42 AM, Nicolas Vervelle nverve...@gmail.comwrote: I usually release the Jmol versions on sourceforge but I am currently out of town. I will probably be able to make the releases on sourceforge by the end of the week. Nico On Wed, Jan 21, 2009 at 7:23 AM, lspri...@weizmann.ac.il wrote: According to Robert Hanson hans...@stolaf.edu: I found both problems and have corrected them for Jmol 11.6.14 and Jmol 11.7.22. Bob Great. Can you please update the sourceforge.net download page or provide an alternative download URL? Thanks again, Jaim -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] How to translate by angstroms
Does anyone know how to translate (in either the x or the y axis) by a specific number of Angstroms? Also is it possible to zoom in/out by a specific number of Angstroms? Thanks, Eran -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] How to translate by angstroms
Hi Eran Translation should be possible using move, if I remember correctly. Not sure about zoom; I think it only works in percent. -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] How to translate by angstroms
Hi Angel, Thanks for the suggestion. I gave it a try, but the translation in the move command also functions via percent as far as I could tell (I gave it a translation of 50 in y, and it moves 50% of the molecule off of the screen. 100% moves 100% off of the screen.) I need a way to translate/zoom using angstroms -- or else a way to convert between angstroms and Jmol percentages which I could do on my own. Thanks, Eran On Wed, Jan 21, 2009 at 5:27 PM, Angel Herraez angel.herr...@uah.es wrote: Hi Eran Translation should be possible using move, if I remember correctly. Not sure about zoom; I think it only works in percent. -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] How to translate by angstroms
Eran, the zoom is by percent, where 100% is the distance of the edge
of a cube containing the entire model. So zoom 100% allows full
rotation of the model within the window (provided you also SET
ZOOMLARGE FALSE) And 50% gets you twice the width as zoom 100%. These
dimensions can be determined by looking at
$ getproperty boundboxinfo
boundboxinfo
center {10.5935 10.2105 6.0790005}
vector {13.6905 10.7265005 13.500999}
corner1 {24.284 20.937 19.58}
corner0 {-3.0970001 -0.51600075 -7.4219995}
or, for example:
$ x=getproperty(boundboxinfo,corner1)
$ print x
{24.284 20.937 19.58}
var x = show(boundbox)
On Wed, Jan 21, 2009 at 7:56 AM, Eran Hodis eranho...@gmail.com wrote:
Does anyone know how to translate (in either the x or the y axis) by a
specific number of Angstroms? Also is it possible to zoom in/out by a
specific number of Angstroms?
It's not exactly clear how that would work with translation, as the
front part is generally at a different scale than the back part, but
perhaps it could be defined in terms of the center. That's an idea.
translate x 0.3 [nm|angstroms]
Thanks,
Eran
--
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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
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Re: [Jmol-users] How to translate by angstroms
Jmol 11.7.22 has a new option for translate:
translate x|y|z x.x nm|angstroms
translate x 2.5 nm
translate y 25 angstroms
translate z 1.0 ang
(only the first character, n or a, is recognized)
For x and y the result is to move the model that many angstroms or
nanometers. For z the result is to change the zoom such that the width
of the display at model center is (approximately) that many angstroms
less -- resulting in the illusion of zoom by that many angstroms. (I
think...you tell me!)
Maximum values are +/-100 units
For now, uploaded to http://chemapps.stolaf.edu/jmol/docs/examples-11
see
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.jar
Bob
On Wed, Jan 21, 2009 at 2:52 PM, Robert Hanson hans...@stolaf.edu wrote:
Eran, the zoom is by percent, where 100% is the distance of the edge
of a cube containing the entire model. So zoom 100% allows full
rotation of the model within the window (provided you also SET
ZOOMLARGE FALSE) And 50% gets you twice the width as zoom 100%. These
dimensions can be determined by looking at
$ getproperty boundboxinfo
boundboxinfo
center {10.5935 10.2105 6.0790005}
vector {13.6905 10.7265005 13.500999}
corner1 {24.284 20.937 19.58}
corner0 {-3.0970001 -0.51600075 -7.4219995}
or, for example:
$ x=getproperty(boundboxinfo,corner1)
$ print x
{24.284 20.937 19.58}
var x = show(boundbox)
On Wed, Jan 21, 2009 at 7:56 AM, Eran Hodis eranho...@gmail.com wrote:
Does anyone know how to translate (in either the x or the y axis) by a
specific number of Angstroms? Also is it possible to zoom in/out by a
specific number of Angstroms?
It's not exactly clear how that would work with translation, as the
front part is generally at a different scale than the back part, but
perhaps it could be defined in terms of the center. That's an idea.
translate x 0.3 [nm|angstroms]
Thanks,
Eran
--
This SF.net email is sponsored by:
SourcForge Community
SourceForge wants to tell your story.
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___
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
--
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
--
This SF.net email is sponsored by:
SourcForge Community
SourceForge wants to tell your story.
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https://lists.sourceforge.net/lists/listinfo/jmol-users
