Re: [Jmol-users] Jmol -- testing requested
Dear Bob, I have tested the Aug 21 Jmol in FirstGlance and the only issue I spotted was the one about fragmentary residues (already reported in a separate email). So it passed with flying colors! Bravo!!! Eric -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Fragmentary residues
This issue is a recent change. These fragmentary residues were properly categorized in Jmol 14.3.7_2014.09.20. On 8/22/15 3:11 PM, Eric Martz wrote: In the PDB format, every atom should be a member of one of these 3 categories: protein, nucleic, hetero. FirstGlance in Jmol has long highlighted any 'anomalous atoms' that do not belong to any of the above 3 categories. It appears to me that Jmol (for a long time, including the latest Aug 17 version) is not properly categorizing certain atoms. They show up as 'anomalous' in FirstGlance (marked with dots and a ? by default). In each case, these are fragments of residues (some main chain atoms are missing). Is this a bug or a feature? Examples: 1flo DC17:H (phosphate only) 4gqj DG6:B 4s0n DT5:E 1h8s GLY112:B, ARG111:A, ALA243:B, ALA243:A (N only) 3eqc ALA220:A, CYS277:A, ASN382:A (N and CA only) In the last case, for example, this leads to the bizarre result select ASN and not protein 2 atoms selected If this is a feature, I can work around it by re-defining 'protein' as the 20 standard L amino acids plus the 20 D amino acids, and 'nucleic' as the standard nucleotides. That will still miss fragments of non-standard residues, but those will be less common. Thanks, Eric -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Dissect PNGJ content?
Thanks, Rolf. I should start a new thread. There are two additional split functions at http://chemapps.stolaf.edu/jmol/docs/index.htm?ver=14.2 , as compared to the split function in your link, and these two contain the “true” parameter. However, the documentation is kind of spare about the need and use for “true” in these additional split functions. I’ll play around with it and start a new thread when I get stuck. Matt On Aug 22, 2015, at 1:42 PM, Rolf Huehne rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de wrote: Am 22.08.15 um 17:23 schrieb Kubasik, Matthew A.: Thanks, Bob, for this. Can you clarify the purpose of “true”, as in: var x = load(“filename”, TRUE) I would like to learn when is it necessary. Your example uses “true” for .png but not for .cif. The help page shows the TRUE flag showing up elsewhere, as in the function x = y.split(, TRUE) I am uncertain of how to use “true properly. The meaning of true as a parameter depends on the specific command/function. You should look up the documentation for the commands/functions you want to use. http://jena3d.fli-leibniz.de/doc/jmol_scripting/index.htm#functions contains for 'x = load(filename,TRUE)': Adding a second parameter TRUE creates a binary associative array variable x that contains the contents of the file. Data are stored as raw bytes (but will appear as a string in the PRINT command). If the file is a standard file, the key _DATA_ will hold the file data. If the file is a PNGJ file, the key _IMAGE_ will hold the image data and additional files will be keyed by file name. If the file is a zip file, the files will be keyed by file name, but no _IMAGE_ key will be present (presumably). Note that x = load(myfile) without TRUE loads just the file list for PNGJ or ZIP files, not the actual data. Regards, Rolf -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Fragmentary residues
In the PDB format, every atom should be a member of one of these 3 categories: protein, nucleic, hetero. FirstGlance in Jmol has long highlighted any 'anomalous atoms' that do not belong to any of the above 3 categories. It appears to me that Jmol (for a long time, including the latest Aug 17 version) is not properly categorizing certain atoms. They show up as 'anomalous' in FirstGlance (marked with dots and a ? by default). In each case, these are fragments of residues (some main chain atoms are missing). Is this a bug or a feature? Examples: 1flo DC17:H (phosphate only) 4gqj DG6:B 4s0n DT5:E 1h8s GLY112:B, ARG111:A, ALA243:B, ALA243:A (N only) 3eqc ALA220:A, CYS277:A, ASN382:A (N and CA only) In the last case, for example, this leads to the bizarre result select ASN and not protein 2 atoms selected If this is a feature, I can work around it by re-defining 'protein' as the 20 standard L amino acids plus the 20 D amino acids, and 'nucleic' as the standard nucleotides. That will still miss fragments of non-standard residues, but those will be less common. Thanks, Eric -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Mouse gestures fail in OS X Firefox Java
Hello all, This is probably just For Your Information (not asking for any fixes from Bob). The problems I'm reporting here appear to be specific to the Java applet in OS X Firefox only. These problems are not seen in JSmol/HTML5 in OS X, *not in Windows 7* nor (except for wheel binding) in OS X Safari or Chrome. I am testing 14.3.16_2015.*08.21* at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED 1. Some default mouse bindings (see 'bind' in the docs) appear to be gone in the Java Applet only. For example, these work in HTML5 but not in the Java applet: SHIFT+LEFT+drag _rotateZorZoom (fails in Firefox 40.0.2, works in Safari, Chrome) WHEEL _wheelZoom (fails in Firefox, Safari, Chrome) Some bindings still work in Firefox: LEFT+drag _slideZoom (right edge of window) LEFT+click _pickAtom LEFT +double +click _setMeasure 2. The following bind command works in HTML5 but not in the Java applet: slab on slab 55 depth 45 bind ALT+SHIFT+LEFT+drag _slabAndDepth (fails in Firefox 40.0.2; works in Safari, Chrome) -Eric -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Dissect PNGJ content?
Am 22.08.15 um 17:23 schrieb Kubasik, Matthew A.: Thanks, Bob, for this. Can you clarify the purpose of “true”, as in: var x = load(“filename”, TRUE) I would like to learn when is it necessary. Your example uses “true” for .png but not for .cif. The help page shows the TRUE flag showing up elsewhere, as in the function x = y.split(, TRUE) I am uncertain of how to use “true properly. The meaning of true as a parameter depends on the specific command/function. You should look up the documentation for the commands/functions you want to use. http://jena3d.fli-leibniz.de/doc/jmol_scripting/index.htm#functions contains for 'x = load(filename,TRUE)': Adding a second parameter TRUE creates a binary associative array variable x that contains the contents of the file. Data are stored as raw bytes (but will appear as a string in the PRINT command). If the file is a standard file, the key _DATA_ will hold the file data. If the file is a PNGJ file, the key _IMAGE_ will hold the image data and additional files will be keyed by file name. If the file is a zip file, the files will be keyed by file name, but no _IMAGE_ key will be present (presumably). Note that x = load(myfile) without TRUE loads just the file list for PNGJ or ZIP files, not the actual data. Regards, Rolf -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Dissect PNGJ content?
Thanks, Bob, for this.
Can you clarify the purpose of “true”, as in:
var x = load(“filename”, TRUE)
I would like to learn when is it necessary. Your example uses “true” for .png
but not for .cif. The help page shows the TRUE flag showing up elsewhere, as
in the function
x = y.split(, TRUE)
I am uncertain of how to use “true properly.
Matt
On Aug 22, 2015, at 12:51 AM, Robert Hanson
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:
http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/Jmol-14.3.16_2015.08.21-binary.zip/download
Jmol.___JmolVersion=14.3.16_2015.08.21
new feature: load var x
-- same as load @x
-- similar in syntax to write var x t.png
-- example:
var x = load(quartz.cif)
load var x {1 1 1}
bug fix: creating and running and saving binary hash from PNGJ fails
-- allows creating an associative binary array from a PNGJ file
then modifying it and loading that variable
then saving it as a new PNGJ file
-- initial PNGJ file is not necessary if binary array x is created first
-- example:
var x = load(test.png,true)
load @x
write test2.png as PNGJ
bug fix: hover callback is not supposed to be stopped with HOVER OFF
bug fix: atom.sx and atom.syhttp://atom.sy/ and atom.szhttp://atom.sz/
report incorrectly when antialiasing is on
bug fix: write VAR x test.png creates a ZIP file instead of a PNGJ file when
x is from load(test.png,true)
bug fix: write test.png as PNGJ (without initial quotes) fails
comments:
OK, that wasn't so bad. Thank you, Rolf, for suggesting this. It is a nice
complement to write var x.
This completes the capability for Jmol or JSmol to read, modify, load, and
save PNGJ and ZIP files.
1) Reading a PNGJ or ZIP file into a variable using TRUE to indicate binary
file:
x = load(test.png, TRUE)
# [x is a binary associative array]
print x.keys
$_BINARY_$
JmolManifest.txt
Jmol_version_14.3.16_2015.08.21__2015-08-21_09.06
_IMAGE_
http___cactus.nci.nih.gov_chemical_structure_caffeine_file_format_sdf_get3d_True
state.spt
where $_BINARY_$ indicates that entries are byte arrays.
and _IMAGE_ is the PNG image, indicating this is from a PNGJ file
2) modifying that file if desired
# coerce to string:
s = + x[state.spt]
# ...modify here...
# replace state.spt in PNGJ file data
x[state.spt] = s
# Or, for example, adding an image that will be used for an optional background
image
x = load(test.png,true)
# a standard binary associative array will have just two keys, $BINARY$ and
_DATA_
# only PNGJ has _IMAGE_
x[z.jpg] = load(z.jpg,true)._DATA_
print x.keys
write var x test3.png
sometime later...
load test3.png
background image test3.png|z.jpg
3) write to a new PNGJ file
write var x test2.png
4) optionally, load that PNGJ data directly from the variable, perhaps to see
that the modifications are correct:
load var x
(new syntax; same as older load @x)
Note that both of these syntaxes work with standard string file data and can be
extended with options:
x = load(quartz.cif)
load var x {1 1 1}
Bob
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Re: [Jmol-users] Hover label - change style (other than font, color and background) and its position
Thanks Robert I will try it.
best regards
Fausto
On 21 August 2015 at 09:29, Robert Hanson hans...@stolaf.edu wrote:
that's it. Could take some ingenuity, but it seems possible to me. Here is
a way to get the coordinate displayed on the document tab of the browser.
Jmol.script(jmolApplet0,set hoverCallback 'myHover';*hover off*)
myHover = function(appletID,label,index){
var app = Jmol._applets[appletID];
var atom = app._applet.viewer.ms.at[index];
var isAntialiased = app._applet.viewer.antialiased;
var sx = atom.sX * (isAntialiased ? 0.5 : 1);
var sy = atom.sY * (isAntialiased ? 0.5 : 1);
var offset = $(app._canvas).offset();
offset.top = Math.floor(offset.top + sy);
offset.left = Math.floor(offset.left + sx);
document.title = JSON.stringify(offset)
}
Notice that we are tapping into JSmol in a way that is not possible in
Java -- going straight into the variables. This is faster, but I don't
generally recommend this.
There is a bug in Jmol right now that when you turn hover off, it does
turn off the callback. That is not supposed to happen. I found the bug, but
it is not available yet, so in the mean time just don't include hover off
for now, or, if you want to go into jsmol/core/corejmol.z.js, you can change
a(!this.hoverEnabled
to
a(!this.hoverEnabled !this.sm.haveHoverCallback()
yourself.
On Thu, Aug 20, 2015 at 5:08 PM, tremato...@gmail.com wrote:
Hi Robert,
Now I understood your suggestion! Disable at jsmol and do it myself using
the data from the hovercallback method. Sorry, I was confused.
best regards
Fausto
On 20 August 2015 at 15:53, Robert Hanson hans...@stolaf.edu wrote:
You will have to turn off the canvas hover that Jmol uses and instead
use your own, totally outside of Jmol.
On Thu, Aug 20, 2015 at 12:43 PM, tremato...@gmail.com wrote:
I'm trying to get there - where the label is - but as it is inside the
canvas element it's hard to inspect. There is a way with chrome experiments
but I can't put to work here. Anyway I will keep trying.
Thanks!
Fausto
On 17 August 2015 at 22:34, Robert Hanson hans...@stolaf.edu wrote:
In order to do that you will need to learn some CSS and JavaScript.
The best way to do this is probably with jQuery. But I do not know exactly
how to do that.
On Mon, Aug 17, 2015 at 10:10 AM, tremato...@gmail.com wrote:
Hello Robert,
Thanks for your explanation, I have been thinking about it but I
still didn't realize how to do it. Could you tell me what kind of return
this callback needs to give to change the hover label position and style?
Have a great day!
Fausto
On 17 August 2015 at 00:59, amitesh sharma siprusha...@gmail.com
wrote:
please describe me how I use in html.
Amitesh kumar sharma
Noida Uttar Pradesh
On Sat, Aug 15, 2015 at 11:56 PM, Robert Hanson hans...@stolaf.edu
wrote:
sorry --
... using jmolApplet0._applet.viewer.ms.at[iatom].sX and ...sY
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Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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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Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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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