Angel, Please check me on the syntax of what I'm suggesting below. I usually do
this with molfiles - not mol2
Birgit,
I'm not sure why you want to store the Jmol mep data in the mol2 file, but here
is an approach that will work. You can store jmol script in a mol2 file that
will automatically
Dear Birgit
The MOL2 format will contain partial charge data for each atom, but not the
MEP. Jmol calculates the MEP coloring from the charges.
I am not sure the MEP data can be saved to file. You can save the
isosurface (with the color map, possibly) from Jmol using either "write
isosurface" c
Birgit-
Those mol2 files probably already have partial charges. To make matters worse,
not all partial charge calculations are the same. That’s going to affect color
and color range. Jmol uses MMFF94 charges.
In my own case, I prefer uniformity in my app, so I go with only Jmol with the
follow
Dear Robert and Angel,your informations are really very interessting. The two commands to calculate and show the MEP ist really easy. But I still have a problem to get the mol2-file.I usually use Avogadro for drawing and then I can save it in different formats. I can even calculate in Avogardo a M
ion for the isosurface comand, have you
> tried that?
>
> http://chemapps.stolaf.edu/jmol/docs/#isosurface
>
>
> Alex
>
> - Ursprüngliche Mail -
> > Von: "Pshemak Maslak"
> > An: jmol-users@lists.sourceforge.net
> > Gesendet: Dienstag, 11.
bruar 2014 16:19:44
> Betreff: [Jmol-users] MEP questions
>
>
> 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
>
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 small
On Fri, May 31, 2013 at 4:27 PM, Pshemak Maslak wrote:
> On 5/31/2013 5:04 PM, Robert Hanson wrote:
>
> In other words, it's Joules.
>
> The numbers displayed are NOT in Jules. (it is e^2 (au)/d (angstrom)).
>
No, of course not. I have no idea what I was referring to there.
>
>
>
> If th
On 5/31/2013 5:04 PM, Robert Hanson wrote:
In other words, it's Joules.
The numbers displayed are NOT in Jules. (it is e^2 (au)/d (angstrom)).
If the charges in the file are in atomic units (multiple of electron
charge) and the distances are measured in angstroms the Jmol
calculated value
In other words, it's Joules.
If the charges in the file are in atomic units (multiple of electron
charge) and the distances are measured in angstroms the Jmol calculated
values of electrostatic potential can be converted into kcal/mol by
multiplying by 332.
>
> I think that is what Jmol does wit
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 * Float.POSITIVE_IN
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 * Float.POSITIVE_INFINITY : x0 / (float)
Math.sqrt(d2));
c
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 * Float.POSITIVE_INFINITY : x0 / (float)
Math.sqrt(d2));
case ONE_OVER_ONE_PLUS_D:
return x0 / (1
When using Spartan, these ranges are set in kcal/mole - i.e. using Spartan to
calculate the MEP.
However, as I mentioned before, because of the seeming inconstancy of charge
units fed to Jmol by various file sources, I wonder if what the Jmol MEP
calculation produces is really a relative energy
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?
T
Otis,
When I go to http://chemagic.com/web_molecules/script_page_large.aspx
and use the menu item surfaces... molecular electrostatic potential
I get a MEP-mapped surface. And when I use my local 12.1.30, it works fine,
as well.
??
Bob
On Sun, Jan 9, 2011 at 9:43 PM, Otis Rothenberger wrote:
anuary 09, 2011 10:59 PM
To: jmol-users@lists.sourceforge.net
Subject: [Jmol-users] MEP Surface Problem
Bob,
Molecular Electrostatic Potential appears to be broken on 12.1.30_dev. I
can't map the surface via the Jmol menu or Jmol script on my page. The Jmol
menu sees that partial charg
Bob,
Molecular Electrostatic Potential appears to be broken on 12.1.30_dev. I
can't map the surface via the Jmol menu or Jmol script on my page. The Jmol
menu sees that partial charges are there, but no mapping occurs.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State Univer
Bob,
I may not understand what should be happening here, so I'll be a bit
more specific.
> It's suppose to load with the same orientation to the viewer that the
> user left it in when saved with Spartan. Is it not doing that? Rotate
> the model in Spartan, save it, and load it into Jmol. Do
On Thu, Sep 16, 2010 at 10:31 AM, Otis Rothenberger
wrote:
> Bob,
>
> Thanks, I think the solution to our ion display issues can be resolved
> with the information you sent. On your one question (end of this email),
> I expected the Jmol default to be reported as the atom charge defaults -
> not
Bob,
Thanks, I think the solution to our ion display issues can be resolved
with the information you sent. On your one question (end of this email),
I expected the Jmol default to be reported as the atom charge defaults -
not the surface charge defaults. This is not a big issue, particularly
Otis -- all about surface types, below.
On Wed, Sep 15, 2010 at 12:24 PM, Otis Rothenberger
wrote:
> Bob,
>
>
> On 9/15/2010 11:47 AM, Robert Hanson wrote:
>
> Charges at atoms have to be summed using q/r for each point on the
> isosurface. So the values at the surface are different from the val
Bob,
On 9/15/2010 11:47 AM, Robert Hanson wrote:
Charges at atoms have to be summed using q/r for each point on the
isosurface. So the values at the surface are different from the values
at the atoms (smaller values). For example:
OK, I get it. The first data range in the message is the data
Charges at atoms have to be summed using q/r for each point on the
isosurface. So the values at the surface are different from the values at
the atoms (smaller values). For example:
$ load c6h6.smol
$ isosurface molecular map mep
isosurface1 created with cutoff=0.0; number of isosurfaces = 1
isosu
Bob,
I'm trying to set a MEP data range for carbocations. I don't understand
an aspect of the Jmol message record. Forgive the tilde's below. They
are to eliminate line breaks in my JavaScript Jmol message trap:
isosurface color range .3 .5 colorscheme 'high' resolution @res vdw 80%
map me
On Mon, Jan 25, 2010 at 1:32 AM, Otis Rothenberger wrote:
> Bob-
>
> 1. New question: We use Accelrys and Spartan to generate data.
> Accerrys calculates partial charge in nC and Spartan calculates this
> charge as esu. I never noticed this before. I assume that as long as
> partial charge sums to
Bob-
While playing around with color range values, I found the source of
one problem, but I still have a couple of questions.
The nitrophenols problem is bad data. I used Accelrys Discovery
Visualizer to draw and calculate these files. For the conanical
structure that I drew, there should have be
I think it would be nice to get a decent set of defaults there. I'm sure I
just guessed.
On Sun, Jan 24, 2010 at 5:43 PM, Otis Rothenberger wrote:
> Bob,
>
> Thanks, that explains it.
>
> Yes, that was JavaScript. I should have mentioned that.
>
> Given your explanation, I think I'm going to play
Bob,
Thanks, that explains it.
Yes, that was JavaScript. I should have mentioned that.
Given your explanation, I think I'm going to play around with reading
partial charges prior to MEP display and then explicitly setting a
specific range based on a JS decision. I'm not sure this is doable,
but
Otis,
[Just to be clear -- those commands you list are being defined in
JavaScript, not Jmol script -- can't do that *exact* command in Jmol script,
right? no " + " there without the script() function or using something
like @colors where colors is a user-defined Jmol variable ]
Yes, MEP. Th
Hello-
I need some advice on MEP display script. When I use the following script:
isosurface COLORSCHEME '" + colors + "'; isosurface resolution 6
MOLECULAR color map mep;isosurface translucent;delay 2; echo;
I get proper MEP's for most molecules, but some molecules present
problems. For exampl
The charge range is beginning to sound familiar. I think I remember
altering this years ago. The relative values of the color range and
charge range are probably what will do the trick. Still have not found
the command parameter but will be experimenting with it. Thanks.
On Nov 11, 2008, at
Altering the values in the color range parameter of the isosurface
command makes the red and blue patches dimmer or brighter. The white
areas increase to some extent because of the diminishing intensity of
the red and blue areas, but the colors get very faint by the time
there is any apprec
Frieda, I'd say that you can set a custom range for charges, then the
color range effectively used will be widened.
(I don't remember the syntax right now.)
-
This SF.Net email is sponsored by the Moblin Your Move Developer'
Are you sure you're just not setting the range to your liking?
On Mon, Nov 10, 2008 at 6:21 PM, Frieda Reichsman <[EMAIL PROTECTED]> wrote:
> Any chance this would be a realistic feature request? For secondary school
> teaching purposes we use the simpler, bwr color scheme that students are
> alr
Any chance this would be a realistic feature request? For secondary
school teaching purposes we use the simpler, bwr color scheme that
students are already familiar with. It can be difficult for some
students to have to shift gears to another scheme. And showing areas
that are hydrophobic i
no, I don't think so.
On Mon, Nov 10, 2008 at 5:46 PM, Frieda Reichsman <[EMAIL PROTECTED]> wrote:
> Hi Bob,
>
> Is there a mechanism, with the rwb or bwr colorshemes, for widening
> the white areas between the red and blue? Many published EP surfaces
> show large neutral regions; I have not figu
Hi Bob,
Is there a mechanism, with the rwb or bwr colorshemes, for widening
the white areas between the red and blue? Many published EP surfaces
show large neutral regions; I have not figured out how to get Jmol to
do this in rwb. These regions are green in the more extended color set.
Than
Try the file, and if you can't
color partialCharges
then let me know.
Bob
rspinney wrote:
>I think your method works well. Will it support other files formats which
>include partial charges?
>
>Rick Spinney
>
>
>
>-
>Take
---
molecular electrostatic potentials
--
*WE NEED TESTERS TO TAKE A CLOSE LOOK AT THIS.*
Jmol 10.9.63 introduces isosurface MEP, with which you can display
molecular electrostatic potentials. These potentials are calculated from
partial charge data present in a fi
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