[Jmol-developers] [ jmol-Feature Requests-1878094 ] Spartan spinput format
Feature Requests item #1878094, was opened at 2008-01-23 07:19 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1878094&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: New IO Format Group: None Status: Open Priority: 5 Private: No Submitted By: Rene Kanters (rkanters) Assigned to: Bob Hanson (hansonr) Summary: Spartan spinput format Initial Comment: Hi, I was wondering whether it is possible to start supporting the Spartan spinput format (which can be created in the windows version of Spartan). It seems very similar to the Odyssey format and in my cases where I have molecules that have a positive charge and S = 1, I have the line 1 2 in the file. If I change this to a 0 1, which is what triggers the resolver to conclude that it is an Odyssey file, the file is read properly. I noticed the email this morning to force load to interpret a file as a cif (where the resolved tripped up), and was wondering whether it maybe possible to resolve this problem/feature request in a similar way too? Thanks, René Just in case somebody is wondering I'll include a spinput file with this request -- >Comment By: Bob Hanson (hansonr) Date: 2008-02-05 07:52 Message: Logged In: YES user_id=1082841 Originator: NO OK, that's checked in for 11.5.4 now. a) ignore comment lines starting with "C " b) check to see that next line starts with " " c) skip one line; check next line for exactly two integers -- charge and spin d) check next line for exactly four numbers Please test using negatively charged species. -- Comment By: Rene Kanters (rkanters) Date: 2008-02-03 14:49 Message: Logged In: YES user_id=905185 Originator: YES The line is basically contains the charge and spin multiplicity (in that order), so the checked in modification of determining whether there are two tokens both of which evaluate to a value larger or equal to 0 would only work for neutral or positive charged ions (not negative ones). I didn't dare to mess with the logic of determining the file format because I wasn't sure what unanticipated consequences my modifications may have on recognizing other file formats, but if it is OK to just verify that the first value is integer and the second larger or equal to 0 the recognition should work. Thanks, René -- Comment By: Bob Hanson (hansonr) Date: 2008-02-01 22:57 Message: Logged In: YES user_id=1082841 Originator: NO What are the options for that line? Anything else besides 0 1 and 1 2 ? This is fixed now for 11.5.4 for those two options, which will be released soon. If other options are possible, then you will have to force the Odyssey reader using: load odyssey::filename.spinput Otherwise Jmol will think this is a MOL file. Bob Hanson -- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1878094&group_id=23629 - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] [ jmol-Feature Requests-1878094 ] Spartan spinput format
Feature Requests item #1878094, was opened at 2008-01-23 08:19 Message generated for change (Comment added) made by rkanters You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1878094&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: New IO Format Group: None Status: Open Priority: 5 Private: No Submitted By: Rene Kanters (rkanters) Assigned to: Bob Hanson (hansonr) Summary: Spartan spinput format Initial Comment: Hi, I was wondering whether it is possible to start supporting the Spartan spinput format (which can be created in the windows version of Spartan). It seems very similar to the Odyssey format and in my cases where I have molecules that have a positive charge and S = 1, I have the line 1 2 in the file. If I change this to a 0 1, which is what triggers the resolver to conclude that it is an Odyssey file, the file is read properly. I noticed the email this morning to force load to interpret a file as a cif (where the resolved tripped up), and was wondering whether it maybe possible to resolve this problem/feature request in a similar way too? Thanks, René Just in case somebody is wondering I'll include a spinput file with this request -- >Comment By: Rene Kanters (rkanters) Date: 2008-02-05 11:54 Message: Logged In: YES user_id=905185 Originator: YES Hi, I just did an update in Eclipse to get the latest modifications, but when I run Jmol I now get the following message: ffa185198:~/Projects/Eclipse/Jmol-datafiles/spinput rkanters$ jmol splash_image=jar:file:/Users/rkanters/Projects/Eclipse/Jmol/build/Jmol.jar!/org/openscience/jmol/images/Jmol_splash.jpg history file is /Users/rkanters/.jmol/history using Smarter Model Adapter (C) 2007 Jmol Development Jmol Version 11.5.4 2007-12-20 00:37 java.vendor:Apple Computer, Inc. java.version:1.5.0_13 os.name:Mac OS X memory:4.3/6.0 appletId: uncaught exception: java.lang.NoSuchMethodError: org.jmol.g3d.Graphics3D.getFont3D(I)Lorg/jmol/g3d/Font3D; java.lang.NoSuchMethodError: org.jmol.g3d.Graphics3D.getFont3D(I)Lorg/jmol/g3d/Font3D; at org.jmol.shape.Measures.initShape(Unknown Source) at org.jmol.shape.Shape.initializeShape(Unknown Source) at org.jmol.modelset.ModelSet.allocateShape(Unknown Source) at org.jmol.modelset.ModelSet.loadShape(Unknown Source) at org.jmol.modelset.ModelLoader.finalizeShapes(Unknown Source) at org.jmol.modelset.ModelLoader.initializeModelSet(Unknown Source) at org.jmol.modelset.ModelLoader.(Unknown Source) at org.jmol.viewer.ModelManager.zap(Unknown Source) at org.jmol.viewer.Viewer.zap(Unknown Source) at org.jmol.viewer.Viewer.setAppletContext(Unknown Source) at org.openscience.jmol.app.Jmol.(Unknown Source) at org.openscience.jmol.app.Jmol.(Unknown Source) at org.openscience.jmol.app.Jmol.getJmol(Unknown Source) at org.openscience.jmol.app.Jmol.main(Unknown Source) Exception in thread "main" java.lang.NullPointerException at org.openscience.jmol.app.Jmol.main(Unknown Source) so something got broken. -- Comment By: Bob Hanson (hansonr) Date: 2008-02-05 08:52 Message: Logged In: YES user_id=1082841 Originator: NO OK, that's checked in for 11.5.4 now. a) ignore comment lines starting with "C " b) check to see that next line starts with " " c) skip one line; check next line for exactly two integers -- charge and spin d) check next line for exactly four numbers Please test using negatively charged species. -- Comment By: Rene Kanters (rkanters) Date: 2008-02-03 15:49 Message: Logged In: YES user_id=905185 Originator: YES The line is basically contains the charge and spin multiplicity (in that order), so the checked in modification of determining whether there are two tokens both of which evaluate to a value larger or equal to 0 would only work for neutral or positive charged ions (not negative ones). I didn't dare to mess with the logic of determining the file format because I wasn't sure what unanticipated consequences my modifications may have on recognizing other file formats, but if it is OK to just verify that the first value is integer and the second larger or equal to 0 the recognition should work. Thanks, René -- Comment By: Bob Hanson (hansonr) Date: 2008-02-01 23:57 Message: Logged In: YES user_id=1082841 Originator: NO What are the options for that line? Anything else besides 0 1 and 1 2 ? This is fixed now for 11.5.4 for those two options, which will be released soon. If other options are possible, then you will have to fo
[Jmol-developers] testing please -- set fontScaling TRUE/FALSE
Jmol Developers -- I need testers. I have uploaded 11.5.4 code that
(1) allows for the fonts in labels and 3D echos to scale with zoom and
window resizing, and
(2) generates proper-sized fonts when an image is created at a different
size than the current window.
This was rather tricky to implement, and I'm not convinced it is
correct. But here is the basic idea:
1) Use
set fontScaling TRUE
to initiate font scaling for labels and 3D echo text. This does not
affect any labels or echo text already in place, and it does not affect
2D echo text at all.
Now zoom to some desired level and create a label or 3D echo:
select atomno=1;label
set echo myecho {1 1 1};echo "testing"
Now zoom some more. You should see the fonts scaling properly.
Resize the window. The fonts should scale.
Use
write image 1000 1000 t.jpg
to create an image. Check it -- the fonts should be scaled properly.
Items to check include axes, unitcells, MO titles, quaternion frame
titles -- anything with text.
Note that because the fonts have to appear the way they always would
before, we have to use the same notation as before for indicating fonts.
(I've expanded that to fractional points, though.) And because fonts
have to scale, there is a "reference" scale for them. This reference is
based on the scale of the display, in Angstroms per pixel. This allows
fonts rendered in one window size to appear scaled properly when the
window size is scaled. The value of this reference is calculated
automatically when you introduce a label or 3D echo, and it is saved in
the state. You can see it by using
show state
In which case you will see something like this:
select ({0});
label "%e%i";
font label 20.0 Serif Plain;
set labelScaleReference 0.02;
and
set echo myecho2 {2.0 2.0 2.0}; echo "XX";
font echo 12.0 Serif Bold 0.01;
The number 0.02 indicated as a labelScaleReference and the number 0.01
at the end of the font command are the scale references, in Angstroms
per pixel. The larger this number, the larger the font. You can change
this number on the fly to set the font scaling to anything you want.
Roughly, the letter "X" of a font of scale 10.0 with a scale reference
of 0.1 will by about 1 Angstrom tall at all zoom levels.
The tricky part of all this was that I had to completely rewrite how
antialiasing of display and images affected font size. So that needs
thorough testing. You will notice some slight changes when you resize a
window. This is because the fonts are scaled in 0.1-point increments.
Also tricky was getting the background boxes and offsets correct. Please
test these, and if you see anything odd, let me know.
I'm also concerned about memory with all these extra fonts. So be on the
alert for slower processing or large memory usage.
Navigation mode is a bit odd -- the way that works is that the screen
scale is fixed, and the model passes through it. So there if navigation
mode is set, then fonts do not scale. It probably suggests I need an
additional scaling based on distance from the plane of the observer in
that case, but I'm not there yet, and I really don't know how to do that
yet.
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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[Jmol-developers] [ jmol-Feature Requests-1878094 ] Spartan spinput format
Feature Requests item #1878094, was opened at 2008-01-23 07:19 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1878094&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: New IO Format Group: None Status: Open Priority: 5 Private: No Submitted By: Rene Kanters (rkanters) Assigned to: Bob Hanson (hansonr) Summary: Spartan spinput format Initial Comment: Hi, I was wondering whether it is possible to start supporting the Spartan spinput format (which can be created in the windows version of Spartan). It seems very similar to the Odyssey format and in my cases where I have molecules that have a positive charge and S = 1, I have the line 1 2 in the file. If I change this to a 0 1, which is what triggers the resolver to conclude that it is an Odyssey file, the file is read properly. I noticed the email this morning to force load to interpret a file as a cif (where the resolved tripped up), and was wondering whether it maybe possible to resolve this problem/feature request in a similar way too? Thanks, René Just in case somebody is wondering I'll include a spinput file with this request -- >Comment By: Bob Hanson (hansonr) Date: 2008-02-05 11:10 Message: Logged In: YES user_id=1082841 Originator: NO try updating again, and do a clean build. -- Comment By: Rene Kanters (rkanters) Date: 2008-02-05 10:54 Message: Logged In: YES user_id=905185 Originator: YES Hi, I just did an update in Eclipse to get the latest modifications, but when I run Jmol I now get the following message: ffa185198:~/Projects/Eclipse/Jmol-datafiles/spinput rkanters$ jmol splash_image=jar:file:/Users/rkanters/Projects/Eclipse/Jmol/build/Jmol.jar!/org/openscience/jmol/images/Jmol_splash.jpg history file is /Users/rkanters/.jmol/history using Smarter Model Adapter (C) 2007 Jmol Development Jmol Version 11.5.4 2007-12-20 00:37 java.vendor:Apple Computer, Inc. java.version:1.5.0_13 os.name:Mac OS X memory:4.3/6.0 appletId: uncaught exception: java.lang.NoSuchMethodError: org.jmol.g3d.Graphics3D.getFont3D(I)Lorg/jmol/g3d/Font3D; java.lang.NoSuchMethodError: org.jmol.g3d.Graphics3D.getFont3D(I)Lorg/jmol/g3d/Font3D; at org.jmol.shape.Measures.initShape(Unknown Source) at org.jmol.shape.Shape.initializeShape(Unknown Source) at org.jmol.modelset.ModelSet.allocateShape(Unknown Source) at org.jmol.modelset.ModelSet.loadShape(Unknown Source) at org.jmol.modelset.ModelLoader.finalizeShapes(Unknown Source) at org.jmol.modelset.ModelLoader.initializeModelSet(Unknown Source) at org.jmol.modelset.ModelLoader.(Unknown Source) at org.jmol.viewer.ModelManager.zap(Unknown Source) at org.jmol.viewer.Viewer.zap(Unknown Source) at org.jmol.viewer.Viewer.setAppletContext(Unknown Source) at org.openscience.jmol.app.Jmol.(Unknown Source) at org.openscience.jmol.app.Jmol.(Unknown Source) at org.openscience.jmol.app.Jmol.getJmol(Unknown Source) at org.openscience.jmol.app.Jmol.main(Unknown Source) Exception in thread "main" java.lang.NullPointerException at org.openscience.jmol.app.Jmol.main(Unknown Source) so something got broken. -- Comment By: Bob Hanson (hansonr) Date: 2008-02-05 07:52 Message: Logged In: YES user_id=1082841 Originator: NO OK, that's checked in for 11.5.4 now. a) ignore comment lines starting with "C " b) check to see that next line starts with " " c) skip one line; check next line for exactly two integers -- charge and spin d) check next line for exactly four numbers Please test using negatively charged species. -- Comment By: Rene Kanters (rkanters) Date: 2008-02-03 14:49 Message: Logged In: YES user_id=905185 Originator: YES The line is basically contains the charge and spin multiplicity (in that order), so the checked in modification of determining whether there are two tokens both of which evaluate to a value larger or equal to 0 would only work for neutral or positive charged ions (not negative ones). I didn't dare to mess with the logic of determining the file format because I wasn't sure what unanticipated consequences my modifications may have on recognizing other file formats, but if it is OK to just verify that the first value is integer and the second larger or equal to 0 the recognition should work. Thanks, René -- Comment By: Bob Hanson (hansonr) Date: 2008-02-01 22:57 Message: Logged In: YES user_id=10828
[Jmol-developers] [ jmol-Feature Requests-1878094 ] Spartan spinput format
Feature Requests item #1878094, was opened at 2008-01-23 05:19 Message generated for change (Comment added) made by nobody You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1878094&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: New IO Format Group: None Status: Open Priority: 5 Private: No Submitted By: Rene Kanters (rkanters) Assigned to: Bob Hanson (hansonr) Summary: Spartan spinput format Initial Comment: Hi, I was wondering whether it is possible to start supporting the Spartan spinput format (which can be created in the windows version of Spartan). It seems very similar to the Odyssey format and in my cases where I have molecules that have a positive charge and S = 1, I have the line 1 2 in the file. If I change this to a 0 1, which is what triggers the resolver to conclude that it is an Odyssey file, the file is read properly. I noticed the email this morning to force load to interpret a file as a cif (where the resolved tripped up), and was wondering whether it maybe possible to resolve this problem/feature request in a similar way too? Thanks, René Just in case somebody is wondering I'll include a spinput file with this request -- Comment By: Nobody/Anonymous (nobody) Date: 2008-02-05 10:26 Message: Logged In: NO I checked and it works for neutral, cation and anion structures. When I get around to it, I will upload the test spinput files to the Jmol-datafiles and check to see how to adjust the junit test for the filereaders too. (I have to run to teach a lab right now). Thanks. -- Comment By: Bob Hanson (hansonr) Date: 2008-02-05 09:10 Message: Logged In: YES user_id=1082841 Originator: NO try updating again, and do a clean build. -- Comment By: Rene Kanters (rkanters) Date: 2008-02-05 08:54 Message: Logged In: YES user_id=905185 Originator: YES Hi, I just did an update in Eclipse to get the latest modifications, but when I run Jmol I now get the following message: ffa185198:~/Projects/Eclipse/Jmol-datafiles/spinput rkanters$ jmol splash_image=jar:file:/Users/rkanters/Projects/Eclipse/Jmol/build/Jmol.jar!/org/openscience/jmol/images/Jmol_splash.jpg history file is /Users/rkanters/.jmol/history using Smarter Model Adapter (C) 2007 Jmol Development Jmol Version 11.5.4 2007-12-20 00:37 java.vendor:Apple Computer, Inc. java.version:1.5.0_13 os.name:Mac OS X memory:4.3/6.0 appletId: uncaught exception: java.lang.NoSuchMethodError: org.jmol.g3d.Graphics3D.getFont3D(I)Lorg/jmol/g3d/Font3D; java.lang.NoSuchMethodError: org.jmol.g3d.Graphics3D.getFont3D(I)Lorg/jmol/g3d/Font3D; at org.jmol.shape.Measures.initShape(Unknown Source) at org.jmol.shape.Shape.initializeShape(Unknown Source) at org.jmol.modelset.ModelSet.allocateShape(Unknown Source) at org.jmol.modelset.ModelSet.loadShape(Unknown Source) at org.jmol.modelset.ModelLoader.finalizeShapes(Unknown Source) at org.jmol.modelset.ModelLoader.initializeModelSet(Unknown Source) at org.jmol.modelset.ModelLoader.(Unknown Source) at org.jmol.viewer.ModelManager.zap(Unknown Source) at org.jmol.viewer.Viewer.zap(Unknown Source) at org.jmol.viewer.Viewer.setAppletContext(Unknown Source) at org.openscience.jmol.app.Jmol.(Unknown Source) at org.openscience.jmol.app.Jmol.(Unknown Source) at org.openscience.jmol.app.Jmol.getJmol(Unknown Source) at org.openscience.jmol.app.Jmol.main(Unknown Source) Exception in thread "main" java.lang.NullPointerException at org.openscience.jmol.app.Jmol.main(Unknown Source) so something got broken. -- Comment By: Bob Hanson (hansonr) Date: 2008-02-05 05:52 Message: Logged In: YES user_id=1082841 Originator: NO OK, that's checked in for 11.5.4 now. a) ignore comment lines starting with "C " b) check to see that next line starts with " " c) skip one line; check next line for exactly two integers -- charge and spin d) check next line for exactly four numbers Please test using negatively charged species. -- Comment By: Rene Kanters (rkanters) Date: 2008-02-03 12:49 Message: Logged In: YES user_id=905185 Originator: YES The line is basically contains the charge and spin multiplicity (in that order), so the checked in modification of determining whether there are two tokens both of which evaluate to a value larger or equal to 0 would only work for neutral or positive charged ions (not negative ones). I didn't dare to mess with the logic of determining the file for
Re: [Jmol-developers] testing please -- set fontScaling TRUE/FALSE
Hi Bob,
I did a few tests on revision 8957 from SVN.
The font scaling with zoom and window resize seems to work very well and
really is a big improvement!
Two points I noticed:
1) The axes labels did not scale.
2) The initial font size was not identical for all labels. Although I
didn't change the default font size and all labels were attached to
alpha carbon atoms some of them had only about half the size than
others. While scaling this difference was preserved.
The label section of the state and 2 example labels looked like this:
# label defaults;
select none;
color label none;
background label none;
set labelOffset 4 4;
set labelAlignment left;
set labelPointer off;
font label 13.0 SansSerif Plain;
...
select ({3952});
label " TOPOISOMERASE_I_EUK :%c";
select ({1593});
label " Exon 1.13 :%c";
...
The "TOPOISOMERASE_I_EUK" label was about twice as big as the "Exon
1.13" label.
Regards,
Rolf
Bob Hanson wrote:
> Jmol Developers -- I need testers. I have uploaded 11.5.4 code that
>
> (1) allows for the fonts in labels and 3D echos to scale with zoom and
> window resizing, and
> (2) generates proper-sized fonts when an image is created at a different
> size than the current window.
>
> This was rather tricky to implement, and I'm not convinced it is
> correct. But here is the basic idea:
>
> 1) Use
>
> set fontScaling TRUE
>
> to initiate font scaling for labels and 3D echo text. This does not
> affect any labels or echo text already in place, and it does not affect
> 2D echo text at all.
>
> Now zoom to some desired level and create a label or 3D echo:
>
> select atomno=1;label
> set echo myecho {1 1 1};echo "testing"
>
> Now zoom some more. You should see the fonts scaling properly.
>
> Resize the window. The fonts should scale.
>
> Use
>
> write image 1000 1000 t.jpg
>
> to create an image. Check it -- the fonts should be scaled properly.
> Items to check include axes, unitcells, MO titles, quaternion frame
> titles -- anything with text.
>
> Note that because the fonts have to appear the way they always would
> before, we have to use the same notation as before for indicating fonts.
> (I've expanded that to fractional points, though.) And because fonts
> have to scale, there is a "reference" scale for them. This reference is
> based on the scale of the display, in Angstroms per pixel. This allows
> fonts rendered in one window size to appear scaled properly when the
> window size is scaled. The value of this reference is calculated
> automatically when you introduce a label or 3D echo, and it is saved in
> the state. You can see it by using
>
> show state
>
> In which case you will see something like this:
>
> select ({0});
> label "%e%i";
> font label 20.0 Serif Plain;
> set labelScaleReference 0.02;
>
> and
>
> set echo myecho2 {2.0 2.0 2.0}; echo "XX";
> font echo 12.0 Serif Bold 0.01;
>
> The number 0.02 indicated as a labelScaleReference and the number 0.01
> at the end of the font command are the scale references, in Angstroms
> per pixel. The larger this number, the larger the font. You can change
> this number on the fly to set the font scaling to anything you want.
> Roughly, the letter "X" of a font of scale 10.0 with a scale reference
> of 0.1 will by about 1 Angstrom tall at all zoom levels.
>
> The tricky part of all this was that I had to completely rewrite how
> antialiasing of display and images affected font size. So that needs
> thorough testing. You will notice some slight changes when you resize a
> window. This is because the fonts are scaled in 0.1-point increments.
>
> Also tricky was getting the background boxes and offsets correct. Please
> test these, and if you see anything odd, let me know.
>
> I'm also concerned about memory with all these extra fonts. So be on the
> alert for slower processing or large memory usage.
>
> Navigation mode is a bit odd -- the way that works is that the screen
> scale is fixed, and the model passes through it. So there if navigation
> mode is set, then fonts do not scale. It probably suggests I need an
> additional scaling based on distance from the plane of the observer in
> that case, but I'm not there yet, and I really don't know how to do that
> yet.
>
> Bob
>
>
>
-
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Re: [Jmol-developers] testing please -- set fontScaling TRUE/FALSE
Rolf Huehne wrote:
>Hi Bob,
>
>I did a few tests on revision 8957 from SVN.
>The font scaling with zoom and window resize seems to work very well and
>really is a big improvement!
>
>Two points I noticed:
>
>1) The axes labels did not scale.
>
>
>
On zooming, right? Correct. This is open for discussion, but axes
labels, unit cell information, frame titles -- all these are considered
nonscaling. You should see them scale if you create a JPG of a new size,
though.
>2) The initial font size was not identical for all labels. Although I
>didn't change the default font size and all labels were attached to
>alpha carbon atoms some of them had only about half the size than
>others. While scaling this difference was preserved.
>
>
You definitely created them at the same zoom level? The state
information below suggests that they were created with set fontScaling
false. Better try that again and send both the history and the state
scripts to me.
Bob
>The label section of the state and 2 example labels looked like this:
>
># label defaults;
> select none;
> color label none;
> background label none;
> set labelOffset 4 4;
> set labelAlignment left;
> set labelPointer off;
> font label 13.0 SansSerif Plain;
>
>...
> select ({3952});
> label " TOPOISOMERASE_I_EUK :%c";
> select ({1593});
> label " Exon 1.13 :%c";
>...
>
>The "TOPOISOMERASE_I_EUK" label was about twice as big as the "Exon
>1.13" label.
>
>Regards,
>Rolf
>
>
>Bob Hanson wrote:
>
>
>>Jmol Developers -- I need testers. I have uploaded 11.5.4 code that
>>
>>(1) allows for the fonts in labels and 3D echos to scale with zoom and
>>window resizing, and
>>(2) generates proper-sized fonts when an image is created at a different
>>size than the current window.
>>
>>This was rather tricky to implement, and I'm not convinced it is
>>correct. But here is the basic idea:
>>
>>1) Use
>>
>> set fontScaling TRUE
>>
>>to initiate font scaling for labels and 3D echo text. This does not
>>affect any labels or echo text already in place, and it does not affect
>>2D echo text at all.
>>
>>Now zoom to some desired level and create a label or 3D echo:
>>
>> select atomno=1;label
>> set echo myecho {1 1 1};echo "testing"
>>
>>Now zoom some more. You should see the fonts scaling properly.
>>
>>Resize the window. The fonts should scale.
>>
>>Use
>>
>> write image 1000 1000 t.jpg
>>
>>to create an image. Check it -- the fonts should be scaled properly.
>>Items to check include axes, unitcells, MO titles, quaternion frame
>>titles -- anything with text.
>>
>>Note that because the fonts have to appear the way they always would
>>before, we have to use the same notation as before for indicating fonts.
>>(I've expanded that to fractional points, though.) And because fonts
>>have to scale, there is a "reference" scale for them. This reference is
>>based on the scale of the display, in Angstroms per pixel. This allows
>>fonts rendered in one window size to appear scaled properly when the
>>window size is scaled. The value of this reference is calculated
>>automatically when you introduce a label or 3D echo, and it is saved in
>>the state. You can see it by using
>>
>> show state
>>
>>In which case you will see something like this:
>>
>> select ({0});
>> label "%e%i";
>> font label 20.0 Serif Plain;
>> set labelScaleReference 0.02;
>>
>>and
>>
>> set echo myecho2 {2.0 2.0 2.0}; echo "XX";
>> font echo 12.0 Serif Bold 0.01;
>>
>>The number 0.02 indicated as a labelScaleReference and the number 0.01
>>at the end of the font command are the scale references, in Angstroms
>>per pixel. The larger this number, the larger the font. You can change
>>this number on the fly to set the font scaling to anything you want.
>>Roughly, the letter "X" of a font of scale 10.0 with a scale reference
>>of 0.1 will by about 1 Angstrom tall at all zoom levels.
>>
>>The tricky part of all this was that I had to completely rewrite how
>>antialiasing of display and images affected font size. So that needs
>>thorough testing. You will notice some slight changes when you resize a
>>window. This is because the fonts are scaled in 0.1-point increments.
>>
>>Also tricky was getting the background boxes and offsets correct. Please
>>test these, and if you see anything odd, let me know.
>>
>>I'm also concerned about memory with all these extra fonts. So be on the
>>alert for slower processing or large memory usage.
>>
>>Navigation mode is a bit odd -- the way that works is that the screen
>>scale is fixed, and the model passes through it. So there if navigation
>>mode is set, then fonts do not scale. It probably suggests I need an
>>additional scaling based on distance from the plane of the observer in
>>that case, but I'm not there yet, and I really don't know how to do that
>>yet.
>>
>>Bob
>>
>>
>>
>>
>>
>
>
>-
>This SF.net email is sponsored by: Microsoft
>Defy all challenges.
Re: [Jmol-developers] testing please -- set fontScaling TRUE/FALSE
11.5.4 Just a quick test, but I find that the font family and style on labels are ignored, both before and after "set fontScaling true" That is, "serif", "monospaced", "italic", "bold" all have no effect; all I can get is sansSerif plain. The size can be set OK.. The scaling on zooming works, and it's a nice improvement. Good work! This is a minor glitch, but if I select an atom, apply a label, then activate font scaling, the label does not scale (as described). However, even after deleting the label (label off) that precise atom cannot ever get a scaling label. Is there a way, or one has to resort to reload the model? - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] testing please -- set fontScaling TRUE/FALSE
Angel Herráez wrote: >11.5.4 >Just a quick test, but I find that the font family and style on labels are >ignored, both before >and after "set fontScaling true" > >That is, "serif", "monospaced", "italic", "bold" all have no effect; all I can >get is sansSerif >plain. The size can be set OK.. > > > Hmm. This all worked fine for me: select atomno=1 label "TESTING" font label 30 font label 30 serif font label 30 serif bold >The scaling on zooming works, and it's a nice improvement. Good work! > > >This is a minor glitch, but if I select an atom, apply a label, then activate >font scaling, the >label does not scale (as described). However, even after deleting the label >(label off) that >precise atom cannot ever get a scaling label. Is there a way, or one has to >resort to reload >the model? > > should be a way. For now you can set labelScaleReference yourself to re-activate scaling. > > > >- >This SF.net email is sponsored by: Microsoft >Defy all challenges. Microsoft(R) Visual Studio 2008. >http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ >___ >Jmol-developers mailing list >Jmol-developers@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
