Re: [Jmol-users] I there a problem with isosurfaces in jmol-14.6.4_2016.10.02

[fziegler]

Prof. Hanson:

Nice job with the RS module. I assume at this stage more complex sequence rules 
are not handled, e.g., seqcis precedes seqtrans [(2Z, 5E)-2, 5-heptadien-3-ol] 
and (+)-inositol. Tried them but no RS designation. As to another matter, I 
contacted you in October about the inability of Jmol.jar in Jmol 14.6.4 to 
write jvxl files. I notice that this is still a problem in Jmol-14.12.1. Any 
thoughts? Thanks, Fred Ziegler
> On Oct 30, 2016, at 6:24 PM, Robert Hanson  wrote:
> 
> Sorry for the delay - I don't know of any other reports relating to the 
> console. Certainly nothing new there in a long time -- since the addition of 
> a font scale button. Anyone else having this issue?  --- Jmol.jar 
> specifically.
> ​
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Re: [Jmol-users] I there a problem with isosurfaces in jmol-14.6.4_2016.10.02

[Robert Hanson]

Sorry for the delay - I don't know of any other reports relating to the
console. Certainly nothing new there in a long time -- since the addition
of a font scale button. Anyone else having this issue?  --- Jmol.jar
specifically.
​
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[Jmol-users] Is there a problem with isosurfaces in jmol-14.6.4_2016.10.02?

[fziegler]

I have been using jmol-14.2.9_2014.11.23 to make electrostatic potential maps. 
[See: http://ursula.chem.yale.edu/~chem220/chem220js/StudyAids.html#ESP] 


I use Gaussian to generate cube files. I open jmol.jar>console and type:

$ isosurface cutoff 0.02 filename_den.cub map filename_esp.cub
$ write isosurface filename.jvxl

All is well.

I downloaded jmol-14.6.4_2016.10.02

The console does not appear to work properly. If the line $ isosurface cutoff 
0.02 filename_den.cub map filename_esp.cub is added, blue text appears with 
cutoff 0.0.

Typing $ write isosurface filename.jvxl gives only a return of the prompt $. No 
jvxl file is written. Multiple entries do not work. Jmol.jar must be closed and 
reopened to make an entry. Still no positive result.

I have taken jmol.jar from jmol-14.2.9_2014.11.23 and put it in 
jmol-14.6.4_2016.10.02. It works but places the file in the former Jmol folder. 
I can redirect the jvxl file with write isosurface /Users/…/filename.jvxl.

But this not an advantage. 

Is there a problem with jmol.jar in mol-14.6.4_2016.10.02?

Thanks for your help, Fred Ziegler--
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[Jmol-users] I there a problem with isosurfaces in jmol-14.6.4_2016.10.02

[fziegler]

I have been using jmol-14.2.9_2014.11.23 to make electrostatic potential maps. 
[See: http://ursula.chem.yale.edu/~chem220/chem220js/StudyAids.html#ESP]

I use Gaussian to generate cube files. I open jmol.jar>console and type:

$ isosurface cutoff 0.02 filename_den.cub map filename_esp.cub
$ write isosurface filename.jvxl

All is well.

I downloaded jmol-14.6.4_2016.10.02

The console does not appear to work properly. If the line $ isosurface cutoff 
0.02 filename_den.cub map filename_esp.cub is added, blue text appears with 
cutoff 0.0.

Typing $ write isosurface filename.jvxl gives only a return of the prompt $. No 
jvxl file is written. Multiple entries do not work. Jmol.jar must be closed and 
reopened to make an entry. Still no positive result.

I have taken jmol.jar from jmol-14.2.9_2014.11.23 and put it in 
jmol-14.6.4_2016.10.02. It works but places the file in the former Jmol folder. 
I can redirect the jvxl file with write isosurface /Users/…/filename.jvxl.

But this not an advantage. 

Is there a problem with jmol.jar in mol-14.6.4_2016.10.02?

Thanks for your help, Fred Ziegler
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