[Jmol-users] An Old Problem Comes Back

[Otis Rothenberger]

  
  
Bob,

I'm using 12.1.11_dev. I think a previously fixed problem has
reappeared. See the image below for ethyne loaded from JME:



A "delete hydrogen;calculate hydrogens" on a ethyne also produces an
old problem result:



Otis


-- 
Otis Rothenberger
chemagic.com
  

--
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] MEP Color Range

[Otis Rothenberger]

 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 range for 
the computed surface charge points. If I use "color range all," then the 
following message type is returned:


data range 0.28645405 to 0.5315478 with color scheme spanning 0.28645405
to 0.5315478

The expression "color scheme spanning" takes on the value of the 
calculated surface data range. If however, in the Jmol script, I set a 
color range based on the actual atomic charges, then this "color scheme 
spanning" reports the value of my Jmol script charges. Is this just a 
message reporting peculiarity? If I want to set an actual range in Jmol 
script, are the actual atomic charges the values that I should use as my 
guide?





Right now, Jmol 11 ignores any charges on atoms more than 8 angstroms 
away from a given point, which doesn't mean much for small models. 
More significantly, though, Jmol right now creates a "field" of 
potential around the model and then uses that to map the surface. This 
isn't really necessary -- you can just pick a surface point and sum 
all the q/d from all the atoms. I've just rewritten the code for 12.0 
and 12.1 to do that and will get that in the next release.


Related to this, I'm not sure that I understand varying Jmol surface 
dimensions. Am I correct that these are the options for creating a 
surface to map?


1) Solvent
2) Molecular
3) van der Waals at settable % values

The reason that I ask this is that Spartan creates something called a 
bond surface map, and I'm trying to translate that into Jmol thinking.


Otis


Bob


On Mon, Sep 13, 2010 at 9:10 PM, Otis Rothenberger 
mailto:osrot...@chemagic.com>> wrote:



The data range 0.41223556 to 0.6573585 seems to vary with the partial
charges, but seems unrelated to the actual partial charges. The result
below is for "range all" on the allyl cation and benzyl cation,
respectively. In the snippet above, I was just trying out values other
than "range all."

 full data range 0.41223556 to 0.6573585 with color scheme spanning
0.41223556 to 0.6573585

data range 0.28645405 to 0.5315478 with color scheme spanning
0.28645405
to 0.5315478

All of this is part of my attempt to make Spartan charge numbers work
well with Accelrys charge numbers. Can you give me any information on
the origin of these numbers - calculated from my charges???

Otis

PS
Thanks for the feedback on the array question.

--
Otis Rothenberger
chemagic.com 





--
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net

https://lists.sourceforge.net/lists/listinfo/jmol-users




--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900


--
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev


___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] MEP Color Range

[Robert Hanson]

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
isosurface full data range -0.2244125 to 0.079268284 with color scheme
spanning -0.1 to 0.1
$ print {1.1}.partialcharge.all
0.23929211
-0.23929211
-0.23929211
-0.23929211
-0.23929211
-0.23929211
-0.23929211
0.23929211
0.23929211
0.23929211
0.23929211
0.23929211

The atom charges range from -0.24 to 0.24, but the surface charges range
from -0.22 to 0.08. I think that's because the center of the ring gets a
substantial contribution from each of the 6 carbons and almost nothing from
the hydrogens (which are positive).

This is interesting -- using ESP charges instead of Mulliken charges from
that same file:

$ load c6h6.smol filter "ESPCHARGES"
$ isosurface molecular map mep
isosurface1 created with cutoff=0.0; number of isosurfaces = 1
isosurface full data range -0.13211405 to 0.046650272 with color scheme
spanning -0.1 to 0.1
$ print {1.1}.partialcharge.all
0.1415481
-0.14394641
-0.14394641
-0.1393379
-0.1393379
-0.1393379
-0.1393379
0.1405371
0.1405371
0.1405371
0.1405371
0.1415481

The ESP charges are less polarized.

Right now, Jmol 11 ignores any charges on atoms more than 8 angstroms away
from a given point, which doesn't mean much for small models. More
significantly, though, Jmol right now creates a "field" of potential around
the model and then uses that to map the surface. This isn't really necessary
-- you can just pick a surface point and sum all the q/d from all the atoms.
I've just rewritten the code for 12.0 and 12.1 to do that and will get that
in the next release.

Bob


On Mon, Sep 13, 2010 at 9:10 PM, Otis Rothenberger wrote:

>
> The data range 0.41223556 to 0.6573585 seems to vary with the partial
> charges, but seems unrelated to the actual partial charges. The result
> below is for "range all" on the allyl cation and benzyl cation,
> respectively. In the snippet above, I was just trying out values other
> than "range all."
>
>  full data range 0.41223556 to 0.6573585 with color scheme spanning
> 0.41223556 to 0.6573585
>
> data range 0.28645405 to 0.5315478 with color scheme spanning 0.28645405
> to 0.5315478
>
> All of this is part of my attempt to make Spartan charge numbers work
> well with Accelrys charge numbers. Can you give me any information on
> the origin of these numbers - calculated from my charges???
>
> Otis
>
> PS
> Thanks for the feedback on the array question.
>
> --
> Otis Rothenberger
> chemagic.com
>
>
>
>
>
> --
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users