Timothy Driscoll wrote:
2) We reserve the right to name ANY NEW TOKEN ANYTHING, so whet if in
10.4 we find use for "src". It breaks your page, that's what.
that would be *extremely* unfortunate, unless it happens in such
distant future that Chime and Rasmol compatibility is no longer an
issue. I would argue very strenuously against this position.
reserving keywords is one thing; reserving the entire universe of
strings is not necessary IMO.
I think I probably said that wrong.
Tim, the issue is simply this: It's unlikely that the Jmol team would
know, for example, that a specific user had used "src" (just as an
example). Are we to then consider asking all users "Can we use 'src'
for a command, or are you already using it?" That's what I mean by
being careful with your definitions. Any user defining terms risks
future breaks. That's all I'm saying. I'm personally recommending
tilde (not underscore) because I know for a fact that it is not used
in any Jmol definition, and so that works.
You could do anything you want. As your scripts are particularly
complex (and hard to debug, as you point out) it might be especially
prudent for you to consider something of this nature, where it is
99.9% guaranteed that your definitions do not clash with Jmol tokens
-- current or future.
Example:
A user using Jmol 10.00 quite uses the word "connected" in a definition:
define connected (hydrogen and within(1.2,oxygen))
We added in 10.2
select connected(hydrogen)
The user installs 10.2 and is surprised to find that her page doesn't
work. "Something is wrong with Jmol!"
Is it? What is broken here? What is the preferred solution to this
problem?
Maybe you thought I was saying you should "have" to use tilde. No, I
was saying it might be wise to do so.
I'm not sure what this has to do with RasMol/Chime compatibility. Does
RasMol have a set of definitions that have not already been added to
Jmol as predefined terms? I thought that was a major project completed
long ago.
Bob
I'll check that script. What model do you want me to use?
it would be more useful to know if Jmol can handle residues numbered
zero or not. that way, I can apply some logic to the rest of the pdb
files that have this in place. the script that I sent is merely one
example.
thanks,
tim
Timothy Driscoll wrote:
On May 5, 2006, at 12:28 p, Bob Hanson wrote:
applet.width == 0 -->
screenPixelCount == 0 -->
cameraDistance == 0 -->
> Exception in thread "Thread-47" java.lang.ArithmeticException: /
by zero
Hmm, what's the context? I didn't know that could happen...
well, the full context is complicated. but it crops up
consistently on trying to send the following script to Jmol. my
thought is that the "define ptyr 0d" is a problem?
restrict none
select all
color labels black
#
#
define src (protein)
define srcsh3domain (84-142)
define srcsh2domain (151-246)
define srckinasedomain (259-518)
define srctail (519-533)
define sh3domain (84-142)
define sh2domain (151-246)
define kinasedomain (259-533)
define tail (519-533)
define phosphotyrosine 527
define srcsh2 :a
define peptide :d
define thrtotrpsh2 :f
define grb2peptide :b
define mutantpeptide :b
define wildtypepeptide :d
define mutanttrp (215f and sidechain)
define wildtypethr (72a and sidechain)
define sh2arginine (32a and sidechain)
define ptyr (0d)
define peptideglu (2d and sidechain)
define peptideasn (319b and sidechain)
define peptideptyr (317b and sidechain)
define sh2ile71 (71a and backbone)
define sh2lys60 (60a and backbone)
reset
rotate x 180
rotate z 12
rotate y 19
rotate x -153
zoom 114
set bondmode and
select srcsh2
script colors/fullpurple.spt
select peptide
script colors/fullorange.spt
select srcsh2
script snaps/cartoon.spt
select atomno=508
label Src SH2 domain
font label 14 sans bold
select all
labels off
select srcsh2
script colors/fullgray.spt
select peptide
script snaps/backbone.spt
select (0d and not (*.o, *.c, *.n)), (32a and sidechain) and not
hydrogen
script colors/element.spt
script snaps/wireframe.spt
select atomno=1068
label pTyr
font label 14 sans bold
select atomno=1111
label Src-bound peptide
font label 14 sans bold
set labeloffset -1 5
select atomno=323
label Arginine
font label 14 sans bold
select atomno=508
label Src SH2 domain
font label 14 sans bold
Timothy Driscoll wrote:
hi,
anyone seen this error:
Exception in thread "Thread-47" java.lang.ArithmeticException: /
by zero
at org.jmol.viewer.TransformManager.scaleToScreen
(TransformManager.java:662)
at org.jmol.viewer.Viewer.scaleToScreen(Viewer.java:441)
at org.jmol.viewer.AminoMonomer.findNearestAtomIndex
(AminoMonomer.java:160)
at org.jmol.viewer.Polymer.findNearestAtomIndex(Polymer.java: 348)
at org.jmol.viewer.Mps$Mpspolymer.findNearestAtomIndex
(Mps.java:352)
at org.jmol.viewer.Mps$Mpsmodel.findNearestAtomIndex (Mps.java:
141)
at org.jmol.viewer.Mps.findNearestAtomIndex(Mps.java:93)
at org.jmol.viewer.Frame.findNearestAtomIndex(Frame.java:959)
at org.jmol.viewer.ModelManager.findNearestAtomIndex
(ModelManager.java:288)
at org.jmol.viewer.Viewer.findNearestAtomIndex(Viewer.java: 1159)
at org.jmol.viewer.MouseManager$HoverWatcher.run
(MouseManager.java:546)
at java.lang.Thread.run(Thread.java:613)
I think it might have to do with a residue number of zero but I
can't be sure. any thoughts? does/should Jmol handle residues
with number zero?
yes, should be OK, but that's a thought.
thanks,
tim
--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
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--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
-------------------------------------------------------
Using Tomcat but need to do more? Need to support web services,
security?
Get stuff done quickly with pre-integrated technology to make your
job easier
Download IBM WebSphere Application Server v.1.0.1 based on Apache
Geronimo
http://sel.as-us.falkag.net/sel? cmd=lnk&kid=120709&bid=263057&dat=121642
_______________________________________________
Jmol-developers mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-developers
--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
-------------------------------------------------------
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job easier
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
_______________________________________________
Jmol-developers mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-developers
