Re: [Jmol-users] Requesting electrostatic potential with Rasmol coloring scheme for MOL and CML files

[Bob H. <ha...@st...>]

Martin Slavík wrote:

>In Jmol I really miss displaying electrostatic potential with /Rasmol/ 
>coloring scheme (it is usefull for depicting small variances in partial 
>charges and handy for educational purposes) for every file type.
>
I'm not certain what that coloring scheme is, but it's possible that you 
aren't taking full advantage
of the isosurface command. You can set the range of colors to whatever 
you want, and there are
five or six color schemes. Can you be more specific -- a specific file, 
perhaps?

> In 
>Chime there was a possibility to display electrostatic potential for 
>every file type (eg. MOL), nowdays in Jmol we can display it only for 
>certain file types.
>
No one will tell us what secret the Chime developers used to fake charge 
distributions. So we
made the decision this past summer to not have Jmol do that and instead 
allow for any file
type that has charge data in it already to be displayed. It's a slightly 
different philosophy. But
there are many file types now that are supported, and if you have 
another, I can do that in a day.


>  In addition, for files without appropriate data 
>(MOL, CML), label %P displays partial charge=0 instead of -- or some 
>approximation (as in Accelrys ViewerLite).
>
>  
>
Again, Jmol is not going to get into the approximation business in this 
regard. I think as a
web page developer you just have to know what files you are working with 
and choose file
types that are appropriate. Then you won't have this problem.

>I will enjoy to have possibility to display such rough approximation 
>(electrostatic potential with /Rasmol/ coloring scheme) and/or label for 
>partial charge for files without appropriate data.
>  
>
Not going to happen, sorry. That decision is final - we need the 
appropriate data.
Partially this is so that we can say that when you look at a rendering 
of MEP in Jmol
it reflects what the calculation intended, not some crude approximation 
invented by me.

That's one difference between Jmol and Chime.

Is there a reason you can't have control over using the %P label option 
only when appropriate?

Bob