because OP confessed to writing a manuscript, and it's
probably good to be clear on this point in any publication.
happy new year,
tim
--
timothy driscoll, phd
bioinformatician
cyberinfrastructure division
virgina bioinformatics institute
On Apr 6, 2012, at 4:01 pm, Philip Bays wrote:
I have looked at the page on my Mac (Snow Leopard). It does not work with
Safari, Camino, or omniweb, but does work with Firefox and Chrome. I get the
same black image with the web GL message. I think the browser-compatiobility
page is out
On Apr 6, 2012, at 4:32 pm, Robert Hanson wrote:
Chrome is the same, except Chrome has software rendering, allowing for WebGL
pretty much everywhere.
OK, I get it. So Chrome's WebGL is a fake, essentially, and that explains why
it is absolutely destroying my battery life right now and
http://arstechnica.com/apple/news/2012/04/flashback-trojan-reportedly-controls-half-a-million-macs-and-counting.ars
Flashback trojan reportedly controls half a million Macs and counting
By Jacqui Cheng | Published about 16 hours ago
Variations of the Flashback trojan have reportedly infected
about that.
cheers,
tim
On Apr 5, 2012, at 10:11 AM, Timothy Driscoll wrote:
http://arstechnica.com/apple/news/2012/04/flashback-trojan-reportedly-controls-half-a-million-macs-and-counting.ars
Flashback trojan reportedly controls half a million Macs and counting
By Jacqui Cheng | Published
On Mar 23, 2012, at 3:33 PM, Eric Martz wrote:
I just heard a segment on NPR about hundreds of high schools that are
abandoning textbooks and giving every student an iPad instead. As we
all know, iPads will not run java and so will not run Jmol. What are
people's thoughts on porting Jmol
On Jan 18, 2011, at 12:34 PM, Fco. Javier Modrego wrote:
May this is of some help,
I use to bundle the jar into double clickable mac app using the instructions
in http://www.devdaily.com/apple/mac/java-jar-bundler/ nevertheless this does
not solve the working dir issue.
I think that the
On Apr 28, 2010, at 10:10 AM, Egon Willighagen wrote:
On Wed, Apr 28, 2010 at 3:59 PM, Robert Hanson hans...@stolaf.edu
wrote:
I propose that Jmol 12.0 officially require Java 1.5. This will
allow easy
expansion of several features, including parallel processing, which
we just
On Dec 2, 2009, at 1:33 pm, Brian Moldover wrote:
So do you load the pdb file multiple times? I’m reading the
documentation but obviously not clear on how to do this or I
wouldn’t have asked J
yes, you can load the same pdb file in multiple applets, and restrict
to different models in
Just found Jmol running on a nice Web site here:
http://www.biohealthbase.org/
tim
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I am behindtherabbit:
del.icio.us | last.fm | mojo | twitter | www | brightkite
-
This SF.net email is
.
tim
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, it is
currently offline shrug)
not sure if I helped or not. :-)
tim
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; sorry.
tim
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On Oct 31, 2007, at 4:09 AM, Bob Hanson wrote:
Timothy Driscoll wrote:
hi,
I am using an external data file to apply a roygb color scheme to a
set of atoms. a snippet from an example data file looks like this:
snip
my Jmol script loads this file and colors atoms (column 1
On Oct 30, 2007, at 5:06 PM, Timothy Driscoll wrote:
hi,
I am using an external data file to apply a roygb color scheme to a
set of atoms. a snippet from an example data file looks like this:
apologies; please ignore. this is a duplicate message.
tim
--
Timothy Driscoll
categories first.
perhaps even log-transform them. this will require a bit of work,
though, so I thought I would float it on the list first. can anyone
confirm this hypothesis?
thanks!
tim
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in both applets, but the right-hand applet quickly falls out of synch
with the left (within 15-20 seconds or so). issuing a 'spin off'
stops the left side, but does *not* stop the right side until the
orientations are again in synch.
tim
--
Timothy Driscoll
--
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On May 23, 2007, at 6:59 PM, Bob Hanson wrote:
Timothy Driscoll wrote:
But if you can figure out a scheme that would be reasonable in
terms of
setting up this function wihtin Jmol -- I would want it to be
possible
to designate what applets are to be synced, not just all applets
, and
which are followers?
What happens when a new file gets loaded in one of the applets?
Timothy Driscoll wrote:
hmm. are you listing these as programming issues that must to be
addressed, or are these ways you would want to extend a synch
command, to make it more powerful? if the former, I see
don't really see a problem with
synching all applets on a page; that would be much simpler anyway.
best,
tim
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-0.342 -0.7
Timothy Driscoll wrote:
On May 10, 2007, at 3:54 PM, Bob Hanson wrote:
This is always a royal pain to get right. Certainly looks like a
rotation matrix to me.
It's got the right form. My guess is you put the vector on the
right and
multiply as:
x' = m11*x + m12
in advance.)
tim
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the coordinate
system of the first, I am told that I should apply this matrix to the
xyz coords of the second. I thought this could be done via a simple
matrix multiplication, but apparently not.
can anyone please suggest a reference that deals with this?
thank you,
tim
--
Timothy Driscoll
?
anyway, I'll keep looking.
tim
Timothy Driscoll wrote:
hi,
I have two structures that I have aligned using a program called
MUSTANG. the program gives me a 3x3 transformation matrix like this
one:
0.58 0.805 0.125
0.521-0.484 0.703
0.626-0.342
.
this works quite well. I've tried it in a number of different
structures. nice!
tim
--
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fantastic. this feature will be
immensely useful for my current project! I'll let you know when it
is ready for primetime.
thanks Bob,
tim
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?
tim
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On May 4, 2007, at 4:23 PM, Bob Hanson wrote:
Timothy Driscoll wrote:
On May 4, 2007, at 1:40 PM, Bob Hanson wrote:
You can slab and depth ATOMS in any number of directions based on
miller
planes or any other sort of plane you can imagine. This is an
internal
sort of slabbing. When
On May 2, 2007, at 8:14 PM, Bob Hanson wrote:
I looking for someone who is using the signed applet.
hi Bob,
I have used it, though rarely.
tim
--
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, but how do I
associate a particular charge with the correct atom? for example:
atomnum charge
1-0.33
2 0.32
3 0.55
4-0.55
5 0
thanks for any help,
tim
--
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...
definitely intrigued to see this in action. especially applied to
cavity isosurfaces, my Jmol Feature of the Month for March.
regards,
tim
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Bioinformatics
are generated separately for each model in
the animation - fantastic!
I like the clickable text. that is a great feature for users. is
there any chance at a mouseover event option as well? it would be
icing on the cake. :-)
tim
--
Timothy Driscollem: [EMAIL
!) has internalized some
of what I used to do in javascript, but still. this is a very useful
ability indeed.
tim
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with a max heap size of 1024mb:
java -Xmx1024m -jar /local/java/jmol/Jmol/build/Jmol.jar
I don't know how to do this for applets; sorry.
hope that helps,
tim
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it, run only pieces of it, even debug it, all in Jmol. tab-complete
for script commands? ;-)
tim
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0
| 7 10 1 0
| 7 12 1 0
| 8 9 1 0
| 8 12 1 0
| 11 12 1 0
|M END
|;
/script
tim
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Paul
Research Technician
Mass Spectrometry
o The
/
o Scripps
\
o Research
/
o Institute
Timothy Driscoll wrote:
off the cuff, you may need some quotes around the value for mol, like
this:
var mol =
?php
if ($data['molfile'])
echo '\'param name=loadInline value
send me the source php off-list?
best,
tim
--
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might be to
issue 'restrict none' immediately after the 'load' command.
regards,
tim
--
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Bioinformatics I: M-1 im: molvisions
On Oct 26, 2006, at 1:38 PM, Angel Herraez wrote:
Timothy Driscoll answered to Rajarshi Guha:
* Since Jmol cannot show multiple structures, I need to convert
my SDF
to PDB and concatenate it to the protein PDB. Is this correct?
as far as I know, yes - you will need to concatenate
than a popup.
tim
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All I've
On Oct 20, 2006, at 10:14 AM, [EMAIL PROTECTED] wrote:
Thank You for this one!!! And half way on the road.
There is a slight drawback with this solution. Each time
my generated script contains an error, detected by Jmol,
the execution stops with a compileError:
--* console start *--
sh jmol
!
tim
--
Timothy Driscollem: [EMAIL PROTECTED]
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All I've got now is a long time, and a slow, slow
that effort the program
wouldn't be
any where near as functional. Your work is deeply appreciated.
hear, hear! heartily seconded.
tim
--
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Bioinformatics I: M-1
On Oct 13, 2006, at 11:29 AM, Bob Hanson wrote:
Let's think about this:
1) We want translations, certainly.
2) Lots of us hack the message stream or message reports to respond to
user or other events.
3) We have an established set of pages we don't want to break.
Options:
1) not
, and it will pause (quit, exit,resume) the loop.
is that right?
tim
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On Sep 26, 2006, at 5:48 PM, Bob Hanson wrote:
new command:
write JPEG|PNG|PDF filename.xxx
so you have that in your script file, you do NOT use the noDisplay
option, and there you go!
Any objection to write?
sorry; late to this corner of the party. should this not be 'export'
On Sep 23, 2006, at 9:59 AM, Bob Hanson wrote:
Jmol fails to connect some atoms with covalent bonds where there
should be
connections.
This is an intended feature, not a bug. In many PDB/mmCIF files, the
author has explicitly defined quite a number of bond connections using
CONECT
On Sep 23, 2006, at 8:35 AM, Angel Herraez wrote:
Hi
After Eric's post on Jmol lots of bugs, Bob has added support for
deuterium and tritium --in fact, for any isotopes--. He has chosen
to assign
them helium and lithium colors.
I have proposed on jmol-developers that unique colors are
issue?
tim
--
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http://www.molvisions.com/im: molvisions
usa:virginia:blacksburg tx: [EMAIL PROTECTED]
Anyone who considers
.
is this not happening? or am I wrong about Jmol's behavior here?
best,
tim
--
Timothy Driscollem: [EMAIL PROTECTED]
Virginia Bioinformatics Institute ph: 540-231-3007
Bioinformatics I: M-1 im: molvisions
Washington St
On Sep 21, 2006, at 1:01 PM, Timothy Driscoll wrote:
if I recall correctly, Jmol does not use the group name to determine
membership in the pre-defined set 'protein.' it uses a minimum set
of atoms (i.e., N, C, O, CA). so as long as modified residues still
use the standard nomenclature
atoms
for other molecule types, but we could not hit upon a 'standard' set
of lipid atoms. I think it is a valuable group, and should be added
at some point, but it may require a different mechanism.
tim
--
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Virginia
their sites in
order to use the new features of Jmol-11.js. by default, it should
be seamless for the majority of users, while advanced users can
rename either the old file, or the new file, if desired.
as long as Jmol-11.js is backwards compatible with Jmol.js, of course.
best,
tim
--
Timothy
.
best,
tim
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Anyone who
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Anyone who considers arithmetical
is not possible, since restrict
wipes
out any previous spacefill and wireframe size information. I'm still
thinking about how to do this better, so one can really restrict and
unrestrict.
new commands - hide and show?
:-)
tim
--
Timothy Driscollem: [EMAIL
, that
mucked up my applets (all plug-ins, actually). I deleted the Plug-
Ins folder in my user library and everything worked fine. so, you
might try that.
hope it works!
tim
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in Safari
without trouble (from http://jmol.sourceforge.net/). it sounds like
a site issue; can you provide a url to test that does not work for you?
regards,
tim
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the command: show orientation.
4. copy and paste the 'moveto' part of the response to 3 in your script.
the moveto will move the molecule from any position to the position
defined in 2 using a smooth motion.
hope that helps,
tim
--
Timothy Driscollem: [EMAIL PROTECTED
like the one
above.
I would hence vote for assigning H atoms to backbone set when they
are bound to backbone C, N, O atoms.
Opinions?
so this is also a problem with the protein set as well? I'll have to
go back and see what we did here.
tim
--
Timothy Driscoll
] On Behalf Of Timothy
Driscoll
Sent: Monday, May 22, 2006 10:50 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] save orientation?
On May 22, 2006, at 10:23 p, Samuel Flores wrote:
Hi Guys,
I'm trying to write some code to let the viewer rotate the molecule
to their
liking, then have
;
rotate z 18.5;
Bob, I knew if I mentioned your name often enough, you would provide
a better solution. :-) I would certainly recommend the above in lieu
of callbacks; although I have never had trouble with callbacks
myself, they are problematic in general.
tim
--
Timothy Driscoll
arsenal). the
command gives a well-formed string that is easily parsable.
hth,
tim
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Washington
encountered this a while ago as well. it is returned as an
Object, not a string. and, a word to the wiser ;-), you *must* force
it to a string using the + operator, as Eric describes. no other
method works.
best,
tim
--
Timothy Driscollem: [EMAIL PROTECTED
On May 10, 2006, at 2:07 a, Bob Hanson wrote:
Timothy Driscoll wrote:
hi all,
anyone know if there is an offset for echo, akin to labeloffset?
I found nothing in the script doc, and I tried some obvious
commands without success (well, obvious to me anyway ;-).
thanks!
tim
don't think it is a bug. :-)
tim
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, with just a few script commands, how the binding site
for a ligand behaves across different models. this would be more
difficult if within were restricted by model. not impossible, but
not as elegant in my opinion.
best,
tim
--
Timothy Driscollem: [EMAIL
On May 9, 2006, at 5:21 p, Nicolas Vervelle wrote:
Timothy Driscoll wrote:
On May 9, 2006, at 4:08 p, Nicolas Vervelle wrote:
as one example, it makes scripting multi-model animations much
easier. for instance, I can use this script:
select all
spacefill 30%
wireframe 0.25
select within
hi all,
anyone know if there is an offset for echo, akin to labeloffset? I
found nothing in the script doc, and I tried some obvious commands
without success (well, obvious to me anyway ;-).
thanks!
tim
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for macromolecules, while it
should not necessarily be promoted, it should be supported. (someone
please feel free to correct me, of course.)
I'm pretty sure that is what Miguel is saying above; I just wanted to
add my comments.
best,
tim
--
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On May 7, 2006, at 2:21 p, Bob Hanson wrote:
Timothy Driscoll wrote:
can Jmol support both versions (HG11 and 1HG1) without converting
between them?
If by can you mean could -- Yes, absolutely.
It all has to do with recognizing what's a number and what's not.
Currently, Jmol 10.2
the predefined atoms
sets are discussed. unless it is in there already and I just missed
it. :-)
thanks again,
tim
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,
tim
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Anyone who considers arithmetical methods of producing
On May 5, 2006, at 10:52 p, Timothy Driscoll wrote:
I have a pdb file (ATP) that contains several atom records in the
following format:
HETATM 42 1HN6 ATP 1 5.276 3.765 1.510 1.00 0.00
as far as I can tell, this is valid pdb format. I should be able
to select the above
On May 6, 2006, at 11:41 p, Bob Hanson wrote:
Timothy Driscoll wrote:
would it be possible to add to the script doc a brief description
of how to use 'wildcard' characters (*, ?, others) in atom
expressions? this might prove useful for others as well.
If I knew how to use them, I'd
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Anyone who considers
format. I should be able to
select the above atom with this kind of expression:
select *.1HN6
but Jmol throws a script error (end of expression expected).
can anyone tell what I am doing wrong?
many thanks for any help,
tim
--
Timothy Driscollem: [EMAIL
command) to use the old Chime-style label
behavior, where the labels always appear in front of the entire
structure?
thanks for any help,
tim
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after
posting to this list. I come back and there's a whole thread. :-)
Bob, many (many) thanks for this. set labelsFront is a huge boon!
best,
tim
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it. so technically... :-P
would you settle for a Guinness or two? :-)
tim I'm only a professional in my spare time d
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don't all come at once. the local tavern,
unfortunately, still deals in money. or occasionally in live
chickens. newly minted Jmol features, sadly, are not yet accepted as
currency. :-)
tim still finding new uses for labelsFront d
--
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On Apr 21, 2006, at 7:58 p, Angel Herraez wrote:
It looks to me that you have the applet files on a different branch
folder
../Gallery/JmolApplet0.jar
than the molecule files
gallery/c2h4.xyz
how about case, too? sometimes Gallery = gallery, and sometimes not.
tim
--
Timothy Driscoll
post a message arguing your position.
I see no problem with this change in behavior.
(sorry; I know its late - I'm trying to keep up with the recent
flurry of emails ;-)
tim
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FYI:
Begin forwarded message:
From: Elisabeth Gasteiger [EMAIL PROTECTED]
Date: March 27, 2006 5:13:44 a EST
To: [EMAIL PROTECTED]
Subject: [help #11227] Please add Jmol and PyMol to mol vis tools
Sender Name: Timothy Driscoll
hello,
please add Jmol (http://jmol.sourceforge.net/) and PyMol
be fairly straightforward as well. can you show us some
demo code that fails?
regards,
tim
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bound and unbound structures in a
single file as different models? then you can use Jmol's built-in
anim commands to flip back-and-forth. this is how most of the Chime
modules displayed this kind of thing, in Hg and others.
best,
tim
--
Timothy Driscollem
On Feb 16, 2006, at 5:01 p, [EMAIL PROTECTED] wrote:
Quoting Timothy Driscoll [EMAIL PROTECTED]:
The problem, of course, is not saving or replaying commands -
which is fairly fast - but the number of false starts and dead-
ends that
I think that you are underestimating the requirements
On Feb 16, 2006, at 5:01 p, [EMAIL PROTECTED] wrote:
Quoting Timothy Driscoll [EMAIL PROTECTED]:
The problem, of course, is not saving or replaying commands -
which is fairly fast - but the number of false starts and dead-
ends that
I think that you are underestimating the requirements
on OSX, but I don't know where other systems log such
events.
hope that helps,
tim
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believe, and Miguel said
something like he would rather work on implementing solvent-
accessible surfaces then this feature... :-)
regards,
tim
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else - exactly what
you are proposing, Bob.
as far as querying the applet for its own state - I suppose callbacks
could have a purpose here, though I don't use them as such (I
generally just watch the applets[] array, for example).
regards,
tim
--
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objInfo=getProperty(some property name)
or
var objInfo=getProperty(some property name,some atom selection)
hi Bob,
I think the idea is excellent. I will have to think a bit more about
the implementation before I feel comfortable giving any informed
input...
regards,
tim
--
Timothy Driscoll
models
at the
same time; that way, maybe a scripted animation could be done (static
model 1, altenating the others).
I agree with Angel that this seems to be the missing functionality.
tim
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.
tim
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Timothy Driscollem: [EMAIL PROTECTED]
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Timothy Driscollem: [EMAIL PROTECTED]
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that out - sorry if it muddled the discussion
somewhat.)
Bob, I will get back to you about your most recent proposal, but
can't until later this evening...
tim
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yourself (since it would affect so much of the
existing code); and 3) that there might be an easier way to
accomplish your goal.
regards,
tim
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