On May 5, 2006, at 12:43 p, Bob Hanson wrote:
I HIGHLY recommend that if you are going to get into lots of
defining that you use a tilde.
define ~src (protein)
this is a problem, given the number of definitions that exist in my
scripts alone.
Two reasons:
1) You can always spot YOUR definitions.
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'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
--
Timothy Driscoll em: [EMAIL PROTECTED]
Virginia Bioinformatics Institute ph: 540-231-3007
Bioinformatics I im: molvisions
Washington St., Blacksburg, VA 24061
"Anyone who considers arithmetical methods of producing random digits
is, of course, in a state of sin." - J von Neumann
-------------------------------------------------------
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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
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