Saw it this morning, sniffed it suspiciously, searched for it unsuccessfully on
sourceforge itself, and then proceeded cautiously. Leads to sourceforge
website, filling in subscription information but not asking for any add'l
information, and then just a click to 'confirm'.
Who knows why they
Would use of OpenGL improve performance of transparency of JSmol, if
implemented?
Most smartphones and computers seem to be OpenGL compliant these days and use
of GPUs instead of CPUs for molvis rendering would seem to be logical.
--pb
From: Robert Hanson
Sen
Does translucency work in WebGL version of Jmol?
I was trying out the WebGL version of JSmol and was very impressed with the
fluid movement. However, trying out the WebGL implementation for the Virtual
Museum of Minerals and Molecules, I couldn't get translucency to work for the
polyhedra.
T
These are ionic radii in the sense that Linus Pauling used them for multiple
oxidation states, extended a number of times in the literature, and probably
reaching their pinnacle in the work of Shannon et al, who calculated ionic
radii as a functional of coordination number. See
http://en.wikipe
Correction below.
On 11/22/13, Phillip Barak
wrote:
> On 11/22/13, Robert Hanson wrote:
> > Test of trusted-signed certificate for the full Jmol build
> >
> >
> > http://chemapps.stolaf.edu/jmol/jsmol2/test2.htm?SIGNED
> >
> >
> >
On 11/22/13, Robert Hanson wrote:
> Test of trusted-signed certificate for the full Jmol build
>
>
> http://chemapps.stolaf.edu/jmol/jsmol2/test2.htm?SIGNED
>
>
> Q: Who is the "Publisher" of the certificate?
Integrated Graphics
> Q: How many warning dialogs do you get? Any big yellow box w
spacefill ionic
--pb
On 09/25/12, Pshemak Maslak
wrote:
> Displaying NaCl (from a cif file) shows Na+ sphere bigger than that of
> Cl-. I am assuming that atomic radii are use. Is there ionic radii info
> in Jmol? If so, how can one display it?
>
> PM
>
>
>
>
> --
ing the Jmol (11.9.32_dev) console, after load xxx.cif {5 5 5} select fx > 0.99the console comes back with: script ERROR: bad argument count select >> { << fx } >= 0.99
etc. BobOn Mon, Mar 8, 2010 at 4:11 PM, Phillip Barak > wrote:
This could be dead easy...Let&
This could be dead easy...Let's say I: load xxx.cif {5 5 5}and now want to select the 3x3x3 cells btwn {2 2 2} and {4 4 4}is there a clean way of doing so?--Phil
--
Download Intel® Parallel Studio Eval
Try the new softwar
Just for the sake of clarification, ionic radii were introduced 'back when' by
Miguel (at my prodding) so that inorganic compounds could be properly drawn and
we made use of oxidation numbers for the elements, when specified, to select
the proper Pauling-type crystal radius. This allowed the us
or other molecular visualization _should_ do with such info
except to automagically populate some and not others by some routine to come up
to the desired occupancy level. Anyone else have thoughts on the subject?
--Phillip Barak
Univ of Wisconsin-Madison
p.s.: many thanks to Bob for the outstand
Since Angel has added in coordination numbers, I'll add in Shannon's values
(1976) for comparison, which seem to be the source for some of the 77th edn
values:
- Original Message -
From: Angel Herraez <[EMAIL PROTECTED]>
> In case it is of help, I found in our library a 56th edition (19
er
> than
> the X(2-) numbers?
>
> I'm guessing "O(1-)" is for something like Na2O2, sodium peroxide. But
> still, that makes no sense whatsoever. The reference reads:
>
>* This data is from
>* Handbook of Chemistry and Physics. 48th Ed, 1967-8, p.
- Original Message -
From: Bob Hanson <[EMAIL PROTECTED]>
Date: Sunday, December 9, 2007 7:52 am
Subject: Re: [Jmol-users] user alert: Java Bug
To: jmol-users@lists.sourceforge.net
> Question, are people seeing this problem at
>
> http://chemapps.stolaf.edu/jmol/docs/examples-11/sync2.
- Original Message -
From: Angel Herraez <[EMAIL PROTECTED]>
Date: Friday, November 30, 2007 3:12 am
Subject: Re: [Jmol-users] Handling Isotopes
To: jmol-users@lists.sourceforge.net
> ...
> BTW, I just found that (Elsevier) MDL has changed name again, it is
> Symyx now !?
The ISIS produ
- Original Message -
From: [EMAIL PROTECTED]
Date: Sunday, November 4, 2007 11:37 am
Subject: [Jmol-users] size of ions
To: jmol-users@lists.sourceforge.net
> My question : How can I produce Jmol output where the ions have ionic
> radii, not
> atomic radii ?
spacefill IONIC
Generat
ld set that up with lobes. The
> problem is defining the different directions. sp, sp2, sp3 are hard
> enough to specify. sp3d2 I gave up. These should be able to be set
> up with combinations of isosurface LOBE commands. Give that a try at least.
>
> Phillip Barak wrote:
>
I find the lcaocartoons for sp3 to be easy to use and delightful. Did the
equivalent sp3d2 for octahedral coordination make into 11.2 (perhaps not listed
in the lcao documentation?), or is it planned for a subsequent version?
--Phil
Phillip Barak
UW-Madison
- Original Message -
From: Angel Herraez <[EMAIL PROTECTED]>
Date: Sunday, June 10, 2007 1:36 pm
>
> 4- "Jmol: an open-source Java viewer for three-dimensional chemical
> and biomolecular
> structures."
> (my preferred one for now)
With all the effort that went into the crystallographic
sible?
--Phillip Barak
-
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Well done!! These Jmol 'illustrations' add so much value to the article! I
especially like the 'rock on' option, although spinning is obviously only the
(rather conservative) start for what that might be. What Jmol behaviors might
'rock on' suggest?
--Phillip Bar
Is that why the CIF files from American Mineralogist Crystal Structure
Database [http://rruff.geo.arizona.edu/AMS/amcsd.php], all of which
start w/ "data_global", no longer work with Jmol v. 10.9.74? (v. 10.9.69
and before worked just fine)
--Phillip Barak
- Original Message -
- Original Message -
From: Bob Hanson <[EMAIL PROTECTED]>
> Just move that atom type block up in front of the atom coordinates.
> I
> know, probably shouldn't have to worry about this.
Yes, that makes it work!!
Thanks,
Phil Barak
site_fract_z
> Ca 0.0 0.0 0.0
> C 0.0 0.0 0.25000
> O 0.25670 0.0 0.25000
> loop_
> _atom_type_symbol
> _atom_type_oxidation_number
> Ca 2
> C 4
> O -2
>
>
JPEG?
>
> Firefox 1.5.0.7 WinXP: no image appears ( !? surprising )
WOMM, Firefox 1.5.0.7 WinXP. Yes, Yes, Yes.
-Phillip Barak
-
Take Surveys. Earn Cash. Influence the Future of IT
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Interested parties might also visit the
http://en.wikipedia.org/wiki/Talk:MDL_Chime to see the dispute over the
statement that "Chime has been largely superceded by Jmol..."
Apparently, someone particularly enamored of the Sculpt mode of Chime,
and miffed that the Jmol community has not yet picked
ion_number
Ca 2
C 4
O -2
>From the Jmol code, ionic radii should be:
C+4: 160
O-2: 1320
Ca+2: 990
but with 'spacefill ionic' command, oxygen is smaller than calcium. Ideas?
--Phillip Barak
-
Take Surveys. Earn
appropriatelyfor each ion for a given structure, but maybe this can
> be left to jmol
> 12.00 :-) Jmol 11.00 is pretty complete as it is.
We too left the calculation of the coordination number--and the use of
the Shannon radii--until a later date :-)
--Phillip Barak
>
--
(1969) or Whittaker and Munter (1970) if we had specified the
coordination number as well.
--Phillip Barak
- Original Message -
From: Alan Hewat <[EMAIL PROTECTED]>
Date: Monday, September 25, 2006 9:13 am
Subject: [Jmol-users] Jmol's use of ionic radii
To: jmol-users@lists.sourc
Wasn't it decided a few months ago that the purpose of the odd-numbered
decimals is for experimental releases, so 10.3 for Bob's great work in
developing new features, while even-numbered decimals, such as 10.2,
would be stable, tested public releases and their bugfixes. IIRC, that
was the motivati
> I have produced Chime animations with integrated audio, so
> technologically, it can be done. now how you would 'record' the
> noise of a molecular vibration... you got me. a really tiny ear?
How about a _micro_phone?
--Phil
---
This SF
d after hitting 'reload' one time.
>
Same here using Mozilla on Win2000.
--Phillip Barak
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and mor
> I must weigh in here. I'll be surprised if the hundredths place has
> reasonable significance in any protein crystal structure.
But Jmol is so adept at rendering non-proteins, too! :-)
> Indeed, the
> tenths decimal place is likely weak in many structures. Remember
> also
> that in a di
work fine on that
display, but not on the next. Just looking for an explanation of the odd
behavior...
> Phillip Barak wrote:
>
> > Could this be another
> > Safari/LiveConnect bug related to frames?
> >
> > --Phil Barak
> >
>
> No, this is a general bug
From: timothy driscoll <[EMAIL PROTECTED]>
Date: Monday, August 29, 2005 9:42 am
> >Question: Are iframes "out" in the "frameless" model?
>
> neither iframes nor frames are depricated or obsolete, even in the
> XHTML 1.0 spec (which is what I try to use for validation). so I
> second David in t
From: Bob Hanson <[EMAIL PROTECTED]>
Date: Wednesday, August 24, 2005 11:54 am
>
> I believe that "polyhedra" does not work. Can anyone tell me if you
> can get it
> to work in the latest release (10.00.11) or any, for that matter?
> I'm sure I saw
> it work there before
http://virtual-mus
> Very good start. I like the Periodic Table.
>
> Let me know if you need additional information.
How about the colors used for water, as in WAT HOH and H2O (seems to be
blue in the Jmol default colors), and for OH (seems to render like H)?
I've been all over the constants file and can't pick it
I _know_ there was a page of Jmol default colors at
http://jmol.sf.net/colors but no more. (And the 'colors' link at the
jmol site links to javascript colors,
http://jmol.sourceforge.net/jscolors/)
Any one help with a pointer?
--Phil
---
SF.N
um of Minerals and Molecules: Molecular Visualization
in a Virtual Hands-On Museum', by Phillip Barak and Edward A. Nater,
accepted for publication in J. Nat. Resour. Life Sci. Educ., Vol. 34,
2005 (pg nos tbd)
...the major thrust is the 'Chime period' of our virtual museum, but
describe
> Warren wrote:
> > Posters are the bane of one's existence as a
> > science grad student, since we
> > were expected to present one at virtually every meeting attended
>
> Glad that was somethign that I missed :-)
>
> Thanks for all the info ... I'll be able to put something together.
>
> Migue
> > > hi folks,
> > >
> > > I am still struggling with running multiple Jmol applets on a
> > single page.
> > > after removing the invalid commands from my button scripts,
> the
> > buttons> now work...when I can get the applets to show up at
> all. :-(
> > >
> > > if anyone wants to offer ad
- Original Message -
From: Miguel <[EMAIL PROTECTED]>
Date: Thursday, June 9, 2005 8:42 am
Subject: Re: [Jmol-users] multiple applets-one page woes
>
> > hi folks,
> >
> > I am still struggling with running multiple Jmol applets on a
> single page.
> > after removing the invalid comma
> Restrict does not 'temporarily' disable display so that things can be
> restored later.
> ...
> So, if you want to do the 'opposite' of restrict then you need to
> explicitly turn on the things that you want to see, with the size
> that you
> want.
>
> spacefill 20%;
> wireframe 0.1;
>
I thin
run Mozilla, w/o problem, with webpages containing Jmol
and mol files, all stored on a USB thumbdrive.
--Phillip Barak
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> The good news is that I found my bug, and I *think* that my code is
> nowworking OK for octagons.
six vertices around a central atom? I believe that you are referring to
an octahedron, instead of an octagon.
:-)
--Phil Barak
---
SF email i
think it would be quite a bit of work for me ...
)
> Q: Would it be *really* valuable?
Leave Jmol as a very clever viewer, and let the designers do their best.
--Phillip Barak
---
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Read honest &
> > Who is "frank" anyway?? :-)
>
> :-)
'Surely you jest!"
"Don't call me 'Shirley'", says Groucho.
>
> 'frank' is the term that MDL used for their 'logo' ... 'frank' as in
> 'stamp' ... but I have never really heard it applied to anything other
> that postage.
>
>
> Miguel (='Frank')
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