I can confirm: the command (in bold below) generated the expected closed
CAP surfaces in Jmol and JSmol.
Thanks Bob,
PM
On 4/20/2017 10:34 PM, Robert Hanson wrote:
On Thu, Apr 20, 2017 at 8:35 AM, Pshemak Maslak <n...@psu.edu
<mailto:n...@psu.edu>> wrote:
Bob;
Bob;
I am looking forward to exploring the new R/S and E/Z functionality;
it's a great addition!
Does this version include fix for "/*spacefill ionic;lcaocartoon scale
1.0 CAP unitcell "cpk";spacefill off" */which freezes the Jmol (Java)
and leaves open surfaces (no "cap') on many unticell
Bob;
I am looking forward to exploring the new R/S and E/Z functionality;
it's a great addition.
Does this version include fix for "/*spacefill ionic;lcaocartoon scale
1.0 CAP unitcell "cpk";spacefill off" */which freezes the Jmol (Java)
and leaves open surfaces (no "cap') on many unticell
Is there a way to turn off atom-label tooltips that show on hover (above
an atom)?
I would like to hide their identity in some totally artificial structures.
Thanks,
PM
--
Check out the vibrant tech community on one
Otis and Dean,
I just tested NaCl in JSmol (JavaSript) on a rather old version
(14.4.1). Surprise: it works as intended (no freezing).
I will do more testing.
Otis, I will send you the cif files to your address (list does not allow
attachments).
Thanks,
PM
On 4/10/2017 1:49 PM, Otis
do something like this to get the unit
cell:
save orientation; load "" {444 666 1}; set displayCellParameters
false;restore orientation; unitcell on; display cell=555; center
visible; zoom 200;
Otis
--
Otis Rothenberger
o...@chemagic.org <mailto:o...@chemagic.org>
http://che
:03 AM, Pshemak Maslak (p...@chem.psu.edu
<mailto:p...@chem.psu.edu>) wrote:
Can the "slab" command be used to produce presentations equivalent to
the image linked below?
https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/File:CCC_crystal_cell_(opaque).svg
If so,
:03 AM, Pshemak Maslak (p...@chem.psu.edu
<mailto:p...@chem.psu.edu>) wrote:
Can the "slab" command be used to produce presentations equivalent to
the image linked below?
https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/File:CCC_crystal_cell_(opaque).svg
If so,
Can the "slab" command be used to produce presentations equivalent to
the image linked below?
https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/File:CCC_crystal_cell_(opaque).svg
If so, any suggestions on how to do that would be appreciated.
Thanks,
PM
The liserv does not like zipped files either.
I can provide files for inspection (outside of the list).
Thanks,
PM
On 12/22/2016 12:21 PM, Pshemak Maslak wrote:
Apparently the file is too large for attachment.
I enclose a file for H2 zipped
Thanks,
PM
On 12/22/2016 12:15 PM, Pshemak
, a couple of typos there. If you want to get it fixed right away,
copy http://chemapps.stolaf.edu/jmol/zip/JSmol.min.js to your jsmol
directory.
On Fri, Feb 19, 2016 at 9:04 AM, Pshemak Maslak <n...@psu.edu
<mailto:n...@psu.edu>> wrote:
Jmol version from January added an opti
Jmol version from January added an option to change play_make_live image:
Jmol.___JmolVersion="14.4.1_2016.01.15"
[...]
JSmol: adds Info.makeLiveImage defaults to j2s/img/play_make_live.jpg
I have a few questions:
The default image is no longer visible in version 14.2.1_2016.0115
The new DSSR has base pairs and nucleotide indexed by numbers, For
example (the 9th base-pair):
auxiliaryinfo.models[1].dssr.pairs[9].bp"A-T"
auxiliaryinfo.models[1].dssr.pairs[9].nt1"|1|D|A|10"
auxiliaryinfo.models[1].dssr.pairs[9].nt2"|1|E|T|29"
What is the proper syntax
Thanks Rolf!
PM
Forwarded per Rolf's request
On 01/28/2016 07:08 PM, Pshemak Maslak wrote:
>
> The new DSSR has base pairs and nucleotide indexed by numbers, For
> example (the 9th base-pair):
>
> auxiliaryinfo.models[1].dssr.pairs[9].bp"A-T"
> auxiliaryinfo
On 1/20/2016 5:27 PM, Robert Hanson wrote:
> That sounds right. We get our DSSR analysis from Columbia University,
> and that format did recently change. It was a beta version previously;
> it should be stable now. Sorry for the trouble.
>
> Bob
Which file of the JSmol distribution contains
I have noticed that a script that worked with a version that was current
in March 2015 (14.2.13_2015.03.23) does not work with the latest two (or
more) versions.
Briefly, I have a short DNA fragment in a png file that loads with the
following commands:
load DNAH-2.png;
set showHydrogens
Thanks Rolf. That helps.
PM
On 1/20/2016 2:51 PM, Rolf Huehne wrote:
> On 01/20/2016 07:37 PM, Pshemak Maslak wrote:
>> I have noticed that a script that worked with a version that was current
>> in March 2015 (14.2.13_2015.03.23) does not work with the latest two (or
&g
I second that request. An option to (easily) specify an alternative icon
(residing in a directory outside of Jmol directories) would be great.
Thanks,
PM
On 1/13/2016 11:29 AM, Geoffrey Rowland wrote:
Hi folks
A minor 'cosmetic' suggestion.
I'm increasingly using PNGJ files with the
The deferred applet uses a small image (light blue circular arrow) to
indicate that the model needs to be activated. That image
(play_make_live.jpg) resides in j2s/img subdirectory. It has a tooltip
(activate 3D model) associated with it.
Can that image be replaced with another and its
It looks like my previous post got lost:
To showcase a crystal structure we have a longish tour script composed of
several moveto, rotate, adding and removing labels, changing translucency
(stepwise), etc. Our Tour button starts the cript and toggles to Stop.
Unfortunately we are not able to
We have tour scripts that use several moveto and rotate commands
during the script execution that take a few seconds each. We would like
to add a STOP button that once clicked would terminate the execution of
the tour script, even if it is in the middle of one of the moveto or
rotate steps.
Bob,
We use Jmol/JSmol within Drupal and behind an access wall controlled
by a university-wide system called Web Access. We had a problem with
accessing JSmol instances using Chrome (it worked in Firefox). The issue
coincided with the introduction of the new jsmol.php file (in March).
Using the Jmol Java applet (desktop) I have noticed that when I load a
pdb file (for example 1EHZ.pdb) using load 1EHZ.pdb, some additional
files are fetched. For example (a partial list for 1EHZ):
fetching http://www.rcsb.org/pdb/files/ligand/2MG.cif
2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
I can select GC base pairs within a DNA stretch using:
within(BASEPAIR,GC). Let's say I have 10 such pairs. Is there a way
to select any specific pair from that set?
Thanks,
PM
--
Dive into the World of Parallel
There is a very nice list of defined groups:
http://chemapps.stolaf.edu/jmol/docs/misc/groups.txt.
My question is about the ether group specifically:
define ~etherO oxygen and connected(2,carbon) and not ~carbonylO
define ~ROR ~etherO
Is it possible to make the definition more specific?
). If the geometry from the first
calculation is saved as xyz (for example) and then the point
calculations are carried on that geometry, the partial charge
information can be read by Jmol.
PM
On 9/10/2014 2:03 PM, Pshemak Maslak wrote:
The puzzle is partially solved. It looks like the problem
, Sep 11, 2014 at 1:43 PM, Pshemak Maslak n...@psu.edu
mailto:n...@psu.edu wrote:
Let me start by repeating the original question: is there a way
to get a numerical value of the dipole moment calculated by Jmol
based on the partial charges in the file?
dipole molecular
d
I have run into an issue with displaying molecular dipoles (and finding
their values).
mol2 file (with Mulliken partial charges) will not display (or
calculate) the molecular dipole.
/dipole molecular/ or /dipole calculate molecular/ do nothing (no
error, no display of any kind)
The MEP
I have encountered a problem working with jvxl and zip files.
I have a big spartan file of cholesterol (cholesterol.spartan) with all
MOs calculated. For a web application, I need just charges (for dipole
vector and MEP) and the HOMO and LUMO surfaces.
In Jmol (Java) app I have written
Thanks Angel,
I have missed that in the manual, that is much simpler.
PM
On 8/14/2014 6:35 AM, Angel Herráez wrote:
Hello Pshemak!
if structures are not hard, at least if you have some experience e.g. with
Javascript.
But for your problem you don't need that; the connect command will
I am just starting to explore if/else and related constructs. I would
like to apply it to animations containing multiple frames (=20).
Since I am learning, I will start with a simple example: an animation of
the SN2 reaction between hydroxide and methyl bromide.
I have two parameters of
_H}; contact*model 1.6 *150% {mySet1}
{mySet2}
to display the contact in the proper model.
Third, CONTACT was not set up for allowing model 1.6 as an option.
That's corrected.
Hope to get that uploaded soon.
Bob
On Mon, Aug 4, 2014 at 11:03 PM, Pshemak Maslak n...@psu.edu
mailto:n
You may try the following:
1. uninstall all Java
2. delete all Java directories (I do not know where they are on OS X,
but on Win they are within AppData and within users) with Oracle and Sun
in the name (does OS X has a good search utility?)
3, reinstall Java
These are probably desperation
On 8/5/2014 1:06 PM, Rzepa, Henry S wrote:
On 5 Aug 2014, at 18:01, Pshemak Maslak n...@psu.edu wrote:
You may try the following:
1. uninstall all Java
2. delete all Java directories (I do not know where they are on OS X, but on
Win they are within AppData and within users) with Oracle
} {atomset2}
and if {atomset2} is not present, then same model and not atomset1
is the default.
You can do intramolecular clashes by specifying two distinct
intramolecular atom sets.
For example:
$ load caffeine.xyz
$ contact {_O} {_H}
On Tue, May 6, 2014 at 9:43 AM, Pshemak Maslak n...@psu.edu
There is a very nice command to sync the applets (sync). Is there a
relatively simple way to do mirror sync?
I imagine that the two models (say enantiomers) would be first manually
oriented to give mirror orientation of each other and locked to give
the synced pair.
Perhaps some fine
How can control measure labels (position and font)?
How does set defaultDistanceLabel format work?
What is format in this case?
Thanks,
PM
--
Want fast and easy access to all the code in your enterprise? Index and
I had similar problems (I reported them some time ago). They were
limited to one Windows machine (Win 7, Firefox, Chrome, IE) of 3 tried
(Win 7 and Win 8).
My problem was with the update procedure. It was insufficient to
uninstall the old version, I had to delete (after uninstalling) all
=14.2.3_2014.07.12 works with Java 7.65? Where
can this version be downloaded?
Thanks,
PM
On 7/16/2014 2:19 AM, Rzepa, Henry S wrote:
On 16 Jul 2014, at 04:45, Pshemak Maslak n...@psu.edu wrote:
I can confirm that observations. All my (remaining) Jmol (Java) instances
show as gray squares
I can confirm that observations. All my (remaining) Jmol (Java)
instances show as gray squares. There are no error messages in the
Java console (in fact, loading of the page with the app does not trigger
opening of the console even if it is set up to open).
Other java applets on the same site
On 6/18/2014 7:20 AM, Ravi Raja Merugu wrote:
Thanks Angel, Thats what I thought . But unfortunately I cant import
files from RCSB server if I use unsigned applets right !! and how to
fix that !!, and recently JAVA applets are being blocked for security
issues, if they are unsigned by almost
Can contact command be used to visualize clashes in small molecules
(such as eclipsed CH3/CH3 in butane, for example)?
What would the full command look like?
Thanks,
PM
--
Is your legacy SCM system holding you
On 4/18/2014 5:47 AM, Angel Herráez wrote:
Hi Pshemak
try this:
spacefill ionic;
print {*}.radius.all;
If you want the full list of original values used, you probably need to check
the source code. The Scripting Doc page has a link to an Excel table (it may
be not up to date, I know there
Is it possible to print out ionic radii used by Jmol?
PM
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Graph Databases is the definitive new guide to graph databases and their
applications. Written by three
I can confirm these observations:
At http://chemapps.stolaf.edu/jmol/jsmol/test2.htm caffeine disappear
when rotated with the mouse on Mac (OS X, 10.9.2) in Firefox (28) and in
Safari (7.0.3)
The same site/molecule works fin in Firefox(28)/Win 7.
PM
On 4/13/2014 10:09 PM, Philip Bays
http://chemapps.stolaf.edu/jmol/jsmol/jsv_jme.htm
http://chemapps.stolaf.edu/jmol/jsmol/jsv_predict2.htm
do not work with the newst Jmol version. . Error message:
JSV.exception.JSVException: Error reading data:
java.lang.NullPointerException
Is it Jmol or any of the other servers?
BTW: does
On 3/6/2014 11:23 PM, Robert Hanson wrote:
Do let me know if there are any bugs I've forgotten to fix before
tomorrow afternoon for 14.0.11 and 14.1.11 (will be identical)
Also, some significant success this week in the JSME/JSpecView area
with NMR prediction AND hand-annotated files
I have visualized MEP for NaCl (molecule) in Spartan and in Jmol). In
Spartan, I see MEP mapped on a density surface that correspond to the
expectation of ionic sizes (Na+ small, Cl- big). In Jmol, MEP is mapped
on what appears to be a molecular surface matching atomic sizes (Na big,
Cl
On 1/10/2014 7:13 PM, Robert Hanson wrote:
Let's track this down. I've seen this on iPads, and it seems to me it
should not be happening.
I believe that happens only in Chrome on windows or in Safari on apple
OS (which apparently use the same browser engine).
PM
On Fri, Jan 10, 2014
It looks like translucent is broken in v 14 for lcaoCartoons.
For example, on
http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?USE=HTML5 and loading
water (load data/water.xyz.gz javascript:Jmol.script(jmolApplet0,'load
data/water.xyz.gz'))
select @3
lcaoCartoon scale 1.3 color [97 173 62]
I am referring to: http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?USE=HTML5
Loading spartan (load data/square_planar.spartan) or xyx.gz files (load
data/water.xyz.gz)in Chrome (but not in Firefox) gives an error popup:
JmolCore.js: synchronous binary file transfer is requested but not
Bob,
It appears that mapping on pointillist representation of atomic orbitals
is broken.
It works in v, 12,2 but not in v 13 on 14 of Jmol.
For example:
isosurface atomicOrbital 1 0 0 1 points 5000 2 map atomicOrbital 1 0
0 1
does not work (no errors in script console).
PM
On 8/30/2013 9:00 AM, Angel Herráez wrote:
Dear JSmolers,
As a result of a recent post, I've been playing with the look and feel of the
pop-up menu in JSmol/HTML5
I'd like to share a CSS-customised variation for your comments, individual
adoption or implementation into default JSmol code.
On 10/2/2013 11:58 AM, Robert Hanson wrote:
This is included in both JSmol 13.3.7 and 13.2.7
Bob and Angel: Thanks!
PM
On Wed, Oct 2, 2013 at 10:10 AM, Angel Herráez angel.herr...@uah.es
mailto:angel.herr...@uah.es wrote:
Hello Pshemak
I'm happy you are interested
On 8/18/2013 6:18 AM, Angel Herráez wrote:
I'm not sure I understand the css/printing business.
Me either, but Pshemak said he wanted a substitute image for the
printed version, and seemed to imply that the regular model does not
print.
What I am seeing is indeed that the browser prints
What are the best strategies to have Jmol or JSmol instances replaced
with a static picture when the browser does not have Java or java script
enabled or is on a device that is not capable of handling Jmol/Jsmol?
How can one do the same for for printing browser pages?
Thanks,
PM
/a2jmolb/browse?sn=testSet/1bna_surface/jmol.png,
On Thu, Aug 15, 2013 at 1:24 PM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:
What are the best strategies to have Jmol or JSmol instances replaced
with a static picture when the browser does not have Java
by zero.-:)
PM
On Wed, May 29, 2013 at 11:17 AM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:
I know I have asked this before, but I still cannot figure it out:
What are the MEP units when the rainbow range is set?
I have tried eV, hartrees
On 5/31/2013 2:02 PM, Pshemak Maslak wrote:
On 5/30/2013 9:22 AM, Robert Hanson wrote:
It's whatever units come from this calculation:
public float valueFor(float x0, float d2, int distanceMode) {
switch (distanceMode) {
case ONE_OVER_D:
return (d2 == 0 ? x0
I know I have asked this before, but I still cannot figure it out:
What are the MEP units when the rainbow range is set?
I have tried eV, hartrees, but these do not match pictures usually shown
with the range of -25/+25 kcal/mol or -50/+ 50 kcal/mol.
If they are not energy, what are they?
On 5/24/2013 10:49 AM, Robert Hanson wrote:
On Fri, May 24, 2013 at 9:54 AM, Angel Herráez angel.herr...@uah.es
mailto:angel.herr...@uah.es wrote:
Hello Pshemak
Finally, can the selected groups of atom (ions) be given a name
(ID) so
they could be referred to without
On 5/19/2013 12:25 PM, Otis Rothenberger wrote:
Chen,
The menu command is:
isosurface delete resolution 0 molecular map MEP translucent
This hides an important issue that I don't fully understand because of
seemingly inconsistent charge units in various files. The issue is the
charge range
I am referring to the deferred-applet mode where an initial image is
displayed and with a click on that image the 3D canvas/model is
activated (whether preloaded or not).
I have not tried anything like that yet, just trying to figure out what
the limitations are.
Let's say I have a number of
Can JSmol instance be displayed (and be functional) in a floating window
(pop-up window)?
I do not know the correct terminology, I do not mean a new browser
window, but one than can only float within the browser, like those
generated, for example by HighSlide (http://highslide.com/)
On 4/19/2013 6:05 PM, Robert Hanson wrote:
right -- don't use Chrome for local file access. See the wiki.
This is not a local file, it is on the server.
The same thing happens in FireFox (except I do not have firebug installed).
PM
On Fri, Apr 19, 2013 at 9:38 AM, Pshemak Maslak p
I am practicing with JSmol:
I have a simple script that loads dna.pdb file and executes a couple of
simple commands.
It works well in Java Jmol, but in JSmol in Chrome JS console throws
XMLHttpRequest.responseType cannot be changed for synchronous HTTP(S)
requests made from the window
Is there a bug in JSmol where it ignores background colors in hex?
In the Jmol info JS array, the color property is ignored if the color is
in hex (specifying it as black, or white works though), whereas in
the (Java) Jmol, the color is set properly. (13.1.15_dev from 2013-04-01).
Thanks,
On 4/18/2013 1:40 PM, Robert Hanson wrote:
define hex.
Hexadecimal, for example [xF0F0F0] for gray
PM
On Thu, Apr 18, 2013 at 11:57 AM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:
Is there a bug in JSmol where it ignores background colors in hex
On 3/11/2013 2:18 PM, Robert Hanson wrote:
Since when are they sp2 ? ;)
Since freshman chemistry covered hybridization?
I am guessing that there is no simple fix...
PM
On Mon, Mar 11, 2013 at 12:40 PM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:
On 3/11/2013
On 3/15/2013 1:42 PM, Simone Sturniolo wrote:
I think the point here is that CO2 has simple sp hybridization, not sp2...
We are talking about lone pairs on oxygens (not about carbon hybridization).
PM
2013/3/15 Pshemak Maslak p...@chem.psu.edu mailto:p...@chem.psu.edu
On 3/11/2013 2
.
On Friday, March 15, 2013, Pshemak Maslak wrote:
On 3/15/2013 1:42 PM, Simone Sturniolo wrote:
I think the point here is that CO2 has simple sp hybridization,
not sp2...
We are talking about lone pairs on oxygens (not about carbon
hybridization).
PM
2013/3/15
)
hybridization scheme.
PM
On Fri, Mar 15, 2013 at 12:32 PM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:
On 3/11/2013 2:18 PM, Robert Hanson wrote:
Since when are they sp2 ? ;)
Since freshman chemistry covered hybridization?
I am guessing
On 3/15/2013 4:38 PM, Robert Hanson wrote:
lcaocartoon ID lp1 center {_O}[1] lobe {0 -0.866 -0.5 0.7}
looks to me to be a decent sp2 orbital for which the associated p
orbital is along x.
The first three numbers are the axis direction; the last one is the
ratio of width to length.
On 3/11/2013 12:58 PM, Robert Hanson wrote:
Good catch, Michael. Yes, it's specifically a problem with -sp3d --
easily fixed.
See http://chemapps.stolaf.edu/jmol/Jmol-13.zip and
http://chemapps.stolaf.edu/jmol/jsmol.zip
Bob
I have lcaocartoon-related questions. For CO2 (for example) the
, the lcaoCartoo lonepair generated dots always stay the same
distance apart (adjust their relative position) as the model is
manipulated.
How can I reproduce that lonepair behavior?
Thanks,
PM
On 12/5/2012 2:47 PM, Pshemak Maslak wrote:
The lcaoCartoon command run on CO2 structure (spartan):
select
The lcaoCartoon command run on CO2 structure (spartan):
select @2
lcaoCartoon scale 2.0 color [97 173 62] translucent
lcaoCartoon create sp2b
creates a lobe that is collinear with the O-C-O axis (rather than about
120 degrees from it). lonepair creates similarly positioned pair of dots.
Is
On 10/6/2012 4:43 PM, Robert Hanson wrote:
Oops. Clearly I never tested radio buttons with JmolJSO. Attached is a
new JmolControls.js
Bob
Thanks, but we still cannot make it work.
Now, the call to
c._getRadio()
in Jmol.jmolRadioGroup in JmolApi.js is returning null causing only
the
I need help with a couple of radio buttons:
The current code I'm using is:
var radios = new Array();
radios[0] = [set background [xF0F0F0], light bckg, true];
radios[1] = [set background black, black bckg];
Jmol.jmolRadioGroup(jmol5, radios);
And the error I keep getting is:
Uncaught
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
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On 9/13/2012 12:16 PM, Robert Hanson wrote:
Isn't the latest version 13.1.5?
I am confused. Where can I find 13.1.5?
The bleeding edge ( http://chemapps.stolaf.edu/jmol/) is 13.1.4 HOLD 2012.
PM
On Tue, Sep 11, 2012 at 7:29 PM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu
On 9/11/2012 8:09 PM, Robert Hanson wrote:
working OK for me. Is this app or applet? What script commands are you
giving Jmol to request select atoms with the mouse?
Tested on the *desktop only* 13.1.4 HOLD (2012-9-8) with .spartan files
The atom labels do not show on hover.
The files
On 9/7/2012 1:03 PM, Robert Hanson wrote:
The polyhedron needs a central atom. But you can add that yourself.
The command appears to be undocumented --
assign {attachmentAtom} Symbol {x y z}
For example:
assign atom {atomno=14} Cl {2 3 4}
That position {2 3 4} could also be an average
Is there a way to draw idealized polyhedra for molecules with missing
vertex atoms, for example a tetrahedron for water or ammonia?
PM
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Exclusive live event will cover all the ways
it :-(
Thanks!
PM
On Sun, Jul 1, 2012 at 10:34 PM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:
I have encountered a problem with displaying p orbital cartoons
with matching colors on all atoms of SO2 molecule.
select all
lcaoCartoon create
I have encountered a problem with displaying p orbital cartoons with
matching colors on all atoms of SO2 molecule.
select all
lcaoCartoon create pz
creates one p orbital with opposite color lobes to the other two.
I can individually add p lobes to all three atoms (and adjust the
Did anybody noticed problems with Jmol reading Spartan 10 .spartan
files?
I have observed that the current version of Spartan (10) produces
files that cannot be read by Jmol. The error message reads: no atoms
found. The file opens correctly in Spartan.
The old version files produced by
On 10/10/2011 2:46 PM, Rzepa Henry wrote:
I am loading two MO surfaces thus
load HHa_mo15.xyz;isosurface HHa_mo15.jvxl translucent;isosurface append
HHa_mo17.jvxl translucent;
I want to show the overlap between two MOs. It is of course a 50%
probability that the phases will match to
On 6/22/2011 2:23 PM, Greeves, Nick wrote:
I use Jmol to display atomic and molecular orbitals and it works well.
I would like to be able to render simple atomic orbitals 1s, 2s, 2p as
electron density maps made up of dots.
Is this currently possible and if so what sort of input file would
I have attempted to combine cif files of graphite, diamond and c60
into one file. The new file shows all three models (separately) as
desired. However, each model is displayed off center, and is off
rotation center when manipulated with a mouse,
Is it possible to do the above (combining
I am just beginning to learn and explore display of crystal structures
in Jmol.
For now, I am just looking at elements and their basic crystal lattices.
I have started with excellent Jmol Crystal Symmetry Explorer
(http://chemapps.stolaf.edu/jmol/docs/examples-11/jcse/explore.htm)
[Thank
On 4/1/2011 1:13 PM, Robert Hanson wrote:
It does, and it doesn't always work properly for all metals. So you
may have to do some
connect
commands for a given specific case to get it exactly the way you want it.
I like the brevity of that file format. Is there a good source of
On 4/1/2011 1:24 PM, Paul Pillot wrote:
The Cristallography Open Database is a good open resource for cif files :
http://www.crystallography.net/
-Paul
Thank you: a very good source of cif files, indeed.
PM
--
On 3/24/2011 9:43 AM, Robert Hanson wrote:
I have put up a new web page that uses some very recent capabilities
of Jmol 12.1.41.
http://chemapps.stolaf.edu/jmol/docs/examples-12/motest/
Specifically, you can:
-- drag/drop any Spartan file or QM output into the applet from your
not (obviously) understand how the cone was constructed and
what are the meanings of the volume vectors and how is the origin
defined, so it is all by trial and error].
On Wed, Oct 6, 2010 at 12:30 PM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:
On 10/4/2010 1:14 PM, Robert
I have a general question:
What are the default cutoff values for atomic and molecular orbitals
isosurfaces generated by Jmol. Are they listed somewhere?
Thanks,
PM
--
Beautiful is writing same markup. Internet
, Oct 6, 2010 at 8:12 AM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:
I have a general question:
What are the default cutoff values for atomic and molecular orbitals
isosurfaces generated by Jmol. Are they listed somewhere?
Thanks,
PM
= (1/sqrt(pi))*Z^(3/2)*exp(-Zr)
On Wed, Oct 6, 2010 at 8:57 AM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:
On 10/6/2010 9:24 AM, Robert Hanson wrote:
The Java console reports the cutoff. I think it's 0.05.
I found:
MOs 0.05
atomic
changing these changes size
[]
I can change the origin, or size or make it elliptic (if the vectors are
not the same), but I do not know how to change the opening angle.
Thanks for your help,
PM
On Mon, Oct 4, 2010 at 11:08 AM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote
How can I draw open right cones in Jmole?
For example, how can draw the double cone for nodal surface of 3d(z^2)
orbital?
Thanks, for your help.
PM
--
Start uncovering the many advantages of virtual appliances
and
to try some Jmol
displays in that category (too many toys, not enough time :-))
On Thu, Sep 2, 2010 at 8:01 AM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:
A case of odd outcome.
I have run the following in 12.0.11 and 12.1.9 (and compared to 12.0,8
which I
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