Re: [Jmol-users] Setting dots size ignores selection

[Robert Hanson]

I have modified the documentation:


dots


*Creates a dotted surface around atoms. DOTS ON, DOTS OFF, and DOTS ONLY
act on the currently selected atoms; all others add the currently selected
atoms to the atoms with dots and then apply their settings to all atoms
with dots. See also the geoSurface
 command and
the settings set dotDensity
 and set
dotScale ,
set dotsSelectedOnly
, and
set dotSurface
.*

On Wed, Oct 26, 2016 at 5:22 AM, Rolf Huehne 
wrote:

> Hi all,
>
> it seems that the command 'dots 50%' ignores the current selection
> unexpectedly in Jmol 14.6.4_2016.10.21 (only tested in the latest version).
>
> You can test it at "https://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm"; by
> entering the following example commands into the console:
>
>  Example commands 
> # Step 1
> select all;
> dots on;
>
> # Step 2
> select oxygen;
> dots 50%;
> --
>
> After step 2 the size of the dotted spheres of all atoms is reduced, not
> just of the oxygens, as it is the case for 'spacefill 50%'.
>
> Is this the intended behaviour for 'dots' or is it a bug?
>
> Regards,
> Rolf
>
> 
> --
> The Command Line: Reinvented for Modern Developers
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>



-- 
Robert M. Hanson
Larson-Anderson Professor 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] Setting dots size ignores selection

[Robert Hanson]

It's a documentation error. DOTS only allows one setting of radius for ALL
atoms. A command such as

dots 50%

also executes an implicit "DOTS ON" for the currently selected atoms, but
it then applies that distance for all atoms.

​Pretty sure it has always been that way.

Bob
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Re: [Jmol-users] Regarding usage of POV-ray

[Angel Herráez]

I can confirm what Kuntal was reporting, and also with a different model


So there is a bug
 in PovRay export from Jmol 14.6.4_2016.10.21
Atoms are rendered much bigger. Bonds seem unaffected.


See example:


PNGJ made by Jmol (alanine from NCI):
http://biomodel.uah.es/angel/Jmol/Ala.Jmol.png



PNG produced after PovRay:
http://biomodel.uah.es/angel/Jmol/Ala.pov.png



intermediate files:
http://biomodel.uah.es/angel/Jmol/Ala.pov
http://biomodel.uah.es/angel/Jmol/Ala.pov.ini


  


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Re: [Jmol-users] Regarding usage of POV-ray

[Robert Hanson]

It's a bug in recent version of Jmol...

On Wed, Oct 26, 2016 at 8:41 AM, Angel Herráez  wrote:

> Dear Kuntal
>
> That should not happen.
> Please provide details:
>
> - version of Jmol you are using
> - the Jmol state of you model as you want it rendered -- you can save that
> usingwrite state "filename.spt"and send us the file, so we can
> test the
> PovRay export
>
> 
> --
> The Command Line: Reinvented for Modern Developers
> Did the resurgence of CLI tooling catch you by surprise?
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>



-- 
Robert M. Hanson
Larson-Anderson Professor 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] Regarding usage of POV-ray

[Angel Herráez]

Dear Kuntal

That should not happen.
Please provide details:

- version of Jmol you are using
- the Jmol state of you model as you want it rendered -- you can save that 
usingwrite state "filename.spt"and send us the file, so we can test the 
PovRay export

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[Jmol-users] Regarding usage of POV-ray

[kuntalch]

Dear all,
I am trying to create pictures of my molecules using jmol and Pov ray. 
When I am trying to reduce the size of the atoms and bonds, although it 
is getting reduced in Jmol, but when I am trying to export them in POV 
Ray to generate pictures the size of the atoms getting increased. what 
should I do to get rid of this problem.

Sincerely,
Kuntal

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[Jmol-users] Setting dots size ignores selection

[Rolf Huehne]

Hi all,

it seems that the command 'dots 50%' ignores the current selection 
unexpectedly in Jmol 14.6.4_2016.10.21 (only tested in the latest version).

You can test it at "https://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm"; by 
entering the following example commands into the console:

 Example commands 
# Step 1
select all;
dots on;

# Step 2
select oxygen;
dots 50%;
--

After step 2 the size of the dotted spheres of all atoms is reduced, not 
just of the oxygens, as it is the case for 'spacefill 50%'.

Is this the intended behaviour for 'dots' or is it a bug?

Regards,
Rolf

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