Re: [Jmol-users] molecular dipoles

2014-09-11 Thread Pshemak Maslak 

Thank you.

This was very educational! In the Interactive Script Documentation 
getProperty shapeInfo lists dipoles, but  shapeInfo.txt example 
(http://chemapps.stolaf.edu/jmol/docs/misc/shapeInfo.txt) has no listing 
for dipoles, which confused me (I was looking for ".dipole.obj[1]" or 
equivalent with no luck)  Now, I have discovered that just typing  
getProperty shapeinfo lists the included properties in the console, (but 
only if that property has been previously calculated).  Make sense of 
course.


PM


On 9/11/2014 7:17 PM, Robert Hanson wrote:

Sorry -- deep-sixed this one.

On Thu, Sep 11, 2014 at 1:43 PM, Pshemak Maslak > 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 = getProperty("shapeInfo.Dipoles[1].vector")
x = sqrt(d*d)



On 9/10/2014 2:03 PM, Pshemak Maslak wrote:


Is the mol2 (Sybyl) file a "wrong" format for displaying dipoles?




mol2 should be fine - provided the partial charges are there.


PM








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Re: [Jmol-users] molecular dipoles

2014-09-11 Thread Robert Hanson 
Sorry -- deep-sixed this one.

On Thu, Sep 11, 2014 at 1:43 PM, Pshemak Maslak  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 = getProperty("shapeInfo.Dipoles[1].vector")
x = sqrt(d*d)



On 9/10/2014 2:03 PM, Pshemak Maslak wrote:

> Is the mol2 (Sybyl) file a "wrong" format for displaying dipoles?
>
>
>
mol2 should be fine - provided the partial charges are there.


> PM
>
>
>
>
>
>
>
> --
> Want excitement?
> Manually upgrade your production database.
> When you want reliability, choose Perforce
> Perforce version control. Predictably reliable.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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
--
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Re: [Jmol-users] molecular dipoles

2014-09-11 Thread Pshemak Maslak 
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?



Now back to spartan files (see below).  If the spartan file is generated 
by "double calculations" the charge information in the file is not 
readable by Jmol.


By double calculations I mean (1). a full-optimization using one method 
(density functional for example) that is saved under a different file 
name on which file (2) a point ("energy") calculation is performed with 
another method (HF for example). 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 with 
dipoles originates in (some) spartan files that were saved as mol2 
files with partial charge information included.  I am still trying to 
figure out what the problem is with these spartan files (they 
definitely have charge information, but also do not display dipoles in 
Jmol).


I would still appreciate help with getting the numerical values of 
dipole moments out of Jmol.


What is the command to "print" (view) the numerical value of the 
dipole moment calculated by Jmol?


Thanks,

PM




On 9/9/2014 11:55 AM, Pshemak Maslak wrote:
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 is generated as expected so I assume that partial charges are 
read.


Is the mol2 (Sybyl) file a "wrong" format for displaying dipoles?

PM






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Re: [Jmol-users] molecular dipoles

2014-09-10 Thread Pshemak Maslak 
The puzzle is partially solved.  It looks like the problem with dipoles 
originates in (some) spartan files that were saved as mol2 files with 
partial charge information included.  I am still trying to figure out 
what the problem is with these spartan files (they definitely have 
charge information, but also do not display dipoles in Jmol).


I would still appreciate help with getting the numerical values of 
dipole moments out of Jmol.


What is the command to "print" (view) the numerical value of the dipole 
moment calculated by Jmol?


Thanks,

PM




On 9/9/2014 11:55 AM, Pshemak Maslak wrote:
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 is generated as expected so I assume that partial charges are 
read.


Is the mol2 (Sybyl) file a "wrong" format for displaying dipoles?

PM




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[Jmol-users] molecular dipoles

2014-09-09 Thread Pshemak Maslak 
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 is generated as expected so I assume that partial charges are read.

Is the mol2 (Sybyl) file a "wrong" format for displaying dipoles?

PM


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