Re: [Jmol-users] draw ARC won't stay FIXED during animation
I think I have this fixed. On Mon, Mar 8, 2010 at 8:35 AM, Dean Johnston djohnsto...@gmail.com wrote: I'll post one as soon as I can - my current observations are on a complex page - I'll try and nail it down to the simplest possible case. Dean On Mon, Mar 8, 2010 at 8:59 AM, Robert Hanson hans...@stolaf.edu wrote: example please. I was working there recently. On Sat, Mar 6, 2010 at 9:27 PM, Dean Johnston djohnsto...@gmail.comwrote: Possible bug with newer version of Jmol (11.9.32). I'm finding that the arcs that I'm drawing (with the FIXED option) are popping on and off during animations. This glitch does not appear in Jmol 11.6. Unless the syntax has changed, I think this might be a bug. All other objects created using the DRAW command (lines, planes, cylinders) are just fine -- only the arcs are affected. Dean -- 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 -- 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] displaying the b-factor
color temperature 2010/3/8 Angel Herráez angel.herr...@uah.es If I remember corectly, the b-factor is read using this command: color tenperature -- 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] black-and-white ORTEP diagrams? (was: CCL: Visualizing Software)
On Mon, Mar 8, 2010 at 2:57 PM, Robert Hanson hans...@stolaf.edu wrote: That's ridiculous. Sorry, but to try to go retro on this is just too strange. :) I agree; don't shoot the messenger. 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 -- 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] expression for multiple cells?
On 03/08/10, Robert Hanson hans...@stolaf.edu wrote:Or, you could use xyz fractional coordinates:select fx = 4.01 and fx = 0.99 and fy = 4.01 and fy = 0.99I like the idea of using fractional coordinates instead of calling out all the individual cells. However, am I missing some punctuation? Using the Jmol (11.9.32_dev) console, after load xxx.cif {5 5 5} select fx 0.99the console comes back with: script ERROR: bad argument count select { fx } = 0.99
etc. BobOn Mon, Mar 8, 2010 at 4:11 PM, Phillip Barak pwba...@wisc.edu pwba...@wisc.edu wrote:
This could be dead easy...Let's say I: load xxx.cif {5 5 5}and now want to select the 3x3x3 cells btwn {2 2 2} and {4 4 4}
is there a clean way of doing so?--Phil
--
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.
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-- Robert M. HansonProfessor of ChemistrySt. Olaf College1520 St. Olaf Ave.Northfield, MN 55057http://www.stolaf.edu/people/hansonr
phone: 507-786-3107If 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___
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Re: [Jmol-users] black-and-white ORTEP diagrams? (was : CCL: Visualizing Software)
On Tue, 9 Mar 2010 17:22:39 +0100, Egon Willighagen egon.willigha...@gmail.com wrote: On Mon, Mar 8, 2010 at 2:57 PM, Robert Hanson hans...@stolaf.edu wrote: That's ridiculous. Sorry, but to try to go retro on this is just too strange. :) I agree; don't shoot the messenger. Especially when there is a free program (Mercury) that does a much better job for simple ORTEP plots (and you don't have to work with ORTEP instructions). Rich -- 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] black-and-white ORTEP diagrams? (was: CCL: Visualizing Software)
there you go! On Tue, Mar 9, 2010 at 11:20 AM, r...@ellerbach.com wrote: On Tue, 9 Mar 2010 17:22:39 +0100, Egon Willighagen egon.willigha...@gmail.com wrote: On Mon, Mar 8, 2010 at 2:57 PM, Robert Hanson hans...@stolaf.edu wrote: That's ridiculous. Sorry, but to try to go retro on this is just too strange. :) I agree; don't shoot the messenger. Especially when there is a free program (Mercury) that does a much better job for simple ORTEP plots (and you don't have to work with ORTEP instructions). Rich -- 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] expression for multiple cells?
darn. It's a 11.9 bug.
On Tue, Mar 9, 2010 at 11:08 AM, Phillip Barak pwba...@wisc.edu wrote:
On 03/08/10, *Robert Hanson * hans...@stolaf.edu wrote:
Or, you could use xyz fractional coordinates:
select fx = 4.01 and fx = 0.99 and fy = 4.01 and fy = 0.99
I like the idea of using fractional coordinates instead of calling out all
the individual cells. However, am I missing some punctuation? Using the Jmol
(11.9.32_dev) console, after
load xxx.cif {5 5 5}
select fx 0.99
the console comes back with:
script ERROR: bad argument count
select { fx } = 0.99
etc.
Bob
On Mon, Mar 8, 2010 at 4:11 PM, Phillip Barak pwba...@wisc.edu
pwba...@wisc.edu wrote:
This could be dead easy...
Let's say I:
load xxx.cif {5 5 5}
and now want to select the 3x3x3 cells btwn {2 2 2} and {4 4 4}
is there a clean way of doing so?
--Phil
--
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
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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
--
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
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Re: [Jmol-users] expression for multiple cells?
I'll have that fixed later today -- must teach...
On Tue, Mar 9, 2010 at 11:29 AM, Robert Hanson hans...@stolaf.edu wrote:
darn. It's a 11.9 bug.
On Tue, Mar 9, 2010 at 11:08 AM, Phillip Barak pwba...@wisc.edu wrote:
On 03/08/10, *Robert Hanson * hans...@stolaf.edu wrote:
Or, you could use xyz fractional coordinates:
select fx = 4.01 and fx = 0.99 and fy = 4.01 and fy = 0.99
I like the idea of using fractional coordinates instead of calling out all
the individual cells. However, am I missing some punctuation? Using the Jmol
(11.9.32_dev) console, after
load xxx.cif {5 5 5}
select fx 0.99
the console comes back with:
script ERROR: bad argument count
select { fx } = 0.99
etc.
Bob
On Mon, Mar 8, 2010 at 4:11 PM, Phillip Barak pwba...@wisc.edu
pwba...@wisc.edu wrote:
This could be dead easy...
Let's say I:
load xxx.cif {5 5 5}
and now want to select the 3x3x3 cells btwn {2 2 2} and {4 4 4}
is there a clean way of doing so?
--Phil
--
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 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
--
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
--
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] draw ARC won't stay FIXED during animation
Yep - problem fixed. Thanks, Bob! On Tue, Mar 9, 2010 at 9:18 AM, Robert Hanson hans...@stolaf.edu wrote: I think I have this fixed. On Mon, Mar 8, 2010 at 8:35 AM, Dean Johnston djohnsto...@gmail.comwrote: I'll post one as soon as I can - my current observations are on a complex page - I'll try and nail it down to the simplest possible case. Dean On Mon, Mar 8, 2010 at 8:59 AM, Robert Hanson hans...@stolaf.edu wrote: example please. I was working there recently. On Sat, Mar 6, 2010 at 9:27 PM, Dean Johnston djohnsto...@gmail.comwrote: Possible bug with newer version of Jmol (11.9.32). I'm finding that the arcs that I'm drawing (with the FIXED option) are popping on and off during animations. This glitch does not appear in Jmol 11.6. Unless the syntax has changed, I think this might be a bug. All other objects created using the DRAW command (lines, planes, cylinders) are just fine -- only the arcs are affected. Dean -- 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 -- 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 -- 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
