Re: [Jmol-users] Jmol menu surface : scripting

[陈文瀚]

Thanks very much, guys. What Bob mentioned (color range all) solved my
problems. The thing is a unified color span is hard to define. If the range
is to large, the coloring would be hard to discriminate the compound with
slight partial charge differences. Range all is exactly what I want, which
magnify the differences.

Cheers,

_
Wenhan Chen
School of Chemistry and Molecular Biosciences
The University of Queensland



2013/5/20 Robert Hanson 

> I believe the default range is -0.1 to 0.1 for isosurface MEP:
>
> $ load $caffeine
> $ calculate partialCharge
> $ isosurface molecular map mep
> isosurface1 created with cutoff=0.0; isosurface count: 1
> isosurface full data range -0.15802732 to 0.11532727 with color scheme
> spanning -0.1 to 0.1
>
> The default range is defined so that different models are comparable. But
> you can set that to anything you want:
>
> $ isosurface molecular color range -0.3 0.3 map mep
> isosurface full data range -0.15802732 to 0.11532727 with color scheme
> spanning -0.3 to 0.3
>
> But your problem, Wenhan Chen, is that the menu uses instead:
>
> isosurface delete resolution 0 vdw color range all map MEP translucent;
>
> and the "range all" is causing the inconsistency. I'll add a new menu item
> for that.
>
> Bob
>
>
>
>
>
> On Mon, May 20, 2013 at 2:18 AM, Angel Herráez wrote:
>
>> > >>> using cmd : show isosurface
>> > I am a able to get the default parameters for the color range setting,
>>
>> No. What you get is the parameters for the last isosurface generated (ie
>> the
>> one you get with the menu, if you used that). It is called isosurface1
>> because
>> the menu does not assign a name to it.
>>
>> Try to use the menu and then the command, to see what comes. It's still
>> possible that the color is not specified in that command.
>>
>>
>>
>>
>> --
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>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> 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] Jmol menu surface : scripting

[Robert Hanson]

I believe the default range is -0.1 to 0.1 for isosurface MEP:

$ load $caffeine
$ calculate partialCharge
$ isosurface molecular map mep
isosurface1 created with cutoff=0.0; isosurface count: 1
isosurface full data range -0.15802732 to 0.11532727 with color scheme
spanning -0.1 to 0.1

The default range is defined so that different models are comparable. But
you can set that to anything you want:

$ isosurface molecular color range -0.3 0.3 map mep
isosurface full data range -0.15802732 to 0.11532727 with color scheme
spanning -0.3 to 0.3

But your problem, Wenhan Chen, is that the menu uses instead:

isosurface delete resolution 0 vdw color range all map MEP translucent;

and the "range all" is causing the inconsistency. I'll add a new menu item
for that.

Bob





On Mon, May 20, 2013 at 2:18 AM, Angel Herráez  wrote:

> > >>> using cmd : show isosurface
> > I am a able to get the default parameters for the color range setting,
>
> No. What you get is the parameters for the last isosurface generated (ie
> the
> one you get with the menu, if you used that). It is called isosurface1
> because
> the menu does not assign a name to it.
>
> Try to use the menu and then the command, to see what comes. It's still
> possible that the color is not specified in that command.
>
>
>
>
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-- 
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Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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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] Jmol menu surface : scripting

[Angel Herráez]

> >>> using cmd : show isosurface
> I am a able to get the default parameters for the color range setting, 

No. What you get is the parameters for the last isosurface generated (ie the 
one you get with the menu, if you used that). It is called isosurface1 because 
the menu does not assign a name to it.

Try to use the menu and then the command, to see what comes. It's still 
possible that the color is not specified in that command.



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Re: [Jmol-users] Jmol menu surface : scripting

[Otis Rothenberger]

This script works, and it does paint the colors rygb over the range -.07 to 
0.7, whatever that means! I intend no sarcasm with the ! mark. I've used these 
values for several years. I just don't know what the actual numbers mean in 
charge units. They just work. I arrived at them by trial and error:

isosurface resolution 0 molecular color range -.07 .07 map mep translucent

Try it yourself on the following page:

http://chemagic.com/JSmolVMK.htm

Using the default model (already has charges), paste the above code in the 
script text box and press ENTER. Play with the -.07 .07 range number2, and 
you'll see the affect of these numbers on the MEP.

I should point out that the following works also. The ALL sets the min/max 
based on the min/max in the model. One problem with this approach is that there 
is not cross model absolute (as with -0.07 0.07). Hence the use of ALL lights 
up ethane, ethene, and ethyne like a Christmas tree - full range of red to blue 
in each molecule. By setting an absolute range, you can get meaningful cross 
model MEP comparisons.

isosurface resolution 0 molecular color range all map mep translucent


Otis

--
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o...@chemagic.com
http://chemagic.com




On May 19, 2013, at 8:36 PM, 陈文瀚 wrote:

> Actually, it doesn't matter much how the color range is determined though 
> confounding. If there is a method, it should be able to invoked, is it?
> >>> using cmd : show isosurface
> I am a able to get the default parameters for the color range setting, but it 
> doesn't really solve my question since the isosurface1(the parameters) is
>  only calculated once the menu "electrostatic surface" is called. What I want 
> is to replace menu click.
> 
> 
> 
> 
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Re: [Jmol-users] Jmol menu surface : scripting

[陈文瀚]

Actually, it doesn't matter much how the color range is determined though
confounding. If there is a method, it should be able to invoked, is it?
>>> using cmd : show isosurface
I am a able to get the default parameters for the color range setting, but
it doesn't really solve my question since the isosurface1(the parameters) is
 only calculated once the menu "electrostatic surface" is called. What I
want is to replace menu click.





_
Wenhan Chen
School of Chemistry and Molecular Biosciences
The University of Queensland



2013/5/20 Otis Rothenberger 

> Exactly! I'm confused. I recall trying to make some sense of this in the
> Spartan docs, but I never found a clear answer. In Jmol, I believe that the
> range is intended as a charge mim/max set, but there is a definite lack of
> magnitude consistency in say Spartan vs MMFF94 or Accelrys charges.
>
> The -.07 .07 range is a pure trial and error range. I don't have a clue
> what units are involved here. This is a long standing question for me. Does
> anyone know?
>
> Consider 1-butanol oxygen:
>
> Spartan -0.738399
> MMFF94 -0.6800
> Accelrys -0.3962
>
> I understand that different algorithms are used resulting in different
> charges based on different assumptions, but in some cases I see power of
> ten differences. Color me unit confused.
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On May 19, 2013, at 1:09 PM, Pshemak Maslak wrote:
>
>  On 5/19/2013 12:25 PM, Otis Rothenberger wrote:
>
> Chen,
>
>  The menu command is:
>
>  isosurface delete resolution 0 molecular map MEP translucent
>
>  This hides an important issue that I don't fully understand because of
> seemingly inconsistent charge units in various files. The issue is the
> charge range of painted colors. The above uses a default range that I don't
> know. Angel, do you know the default? By trial and error, I settled on the
> following:
>
>  isosurface resolution 0 molecular color range -.07 .07 map
> mep translucent
>
>
>  Otis
>
>
> BTW: what are the units for MEP?  What is " -0.07" in the example above?
> Is that number for potential energy?   Or just Q/distance? (Q in what
> units, distance in what units)? Or something else?
>
> PM
>
>
>
>
>
>
>
>   --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>  On May 19, 2013, at 11:49 AM, Angel Herráez wrote:
>
>  Hello Chen
>
>  You can try enetering this in the script console just after you use the
> menu option:
>
>  show isosurface
>
>  amongst the long text displayed, there is a section entitled
> 
> which has the script that will render the isosurface you have.
>
>  As for getting a color, you can include the color definition in your
> isosurface script, but sometimes that is a little tricky, and it is always
> safe and easy to apply color in a second command, like e.g.
>
>  isosurface mysurf1 molecular;
> color $mysurf1 translucent* * green;
>
>
> --
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Re: [Jmol-users] Jmol menu surface : scripting

[Otis Rothenberger]

Exactly! I'm confused. I recall trying to make some sense of this in the 
Spartan docs, but I never found a clear answer. In Jmol, I believe that the 
range is intended as a charge mim/max set, but there is a definite lack of 
magnitude consistency in say Spartan vs MMFF94 or Accelrys charges.

The -.07 .07 range is a pure trial and error range. I don't have a clue what 
units are involved here. This is a long standing question for me. Does anyone 
know?

Consider 1-butanol oxygen:

Spartan -0.738399
MMFF94 -0.6800
Accelrys -0.3962

I understand that different algorithms are used resulting in different charges 
based on different assumptions, but in some cases I see power of ten 
differences. Color me unit confused.

Otis

--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com




On May 19, 2013, at 1:09 PM, Pshemak Maslak wrote:

> On 5/19/2013 12:25 PM, Otis Rothenberger wrote:
>> Chen,
>> 
>> The menu command is:
>> 
>> isosurface delete resolution 0 molecular map MEP translucent
>> 
>> This hides an important issue that I don't fully understand because of 
>> seemingly inconsistent charge units in various files. The issue is the 
>> charge range of painted colors. The above uses a default range that I don't 
>> know. Angel, do you know the default? By trial and error, I settled on the 
>> following:
>> 
>> isosurface resolution 0 molecular color range -.07 .07 map mep translucent
>> 
>> 
>> Otis
>> 
> 
> BTW: what are the units for MEP?  What is " -0.07" in the example above?  Is 
> that number for potential energy?   Or just Q/distance? (Q in what units, 
> distance in what units)? Or something else?
> 
> PM
> 
> 
> 
> 
> 
> 
> 
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>> 
>> 
>> On May 19, 2013, at 11:49 AM, Angel Herráez wrote:
>> 
>>> Hello Chen
>>> 
>>> You can try enetering this in the script console just after you use the 
>>> menu option:
>>> 
>>> show isosurface
>>> 
>>> amongst the long text displayed, there is a section entitled
>>> 
>>> which has the script that will render the isosurface you have.
>>> 
>>> As for getting a color, you can include the color definition in your 
>>> isosurface script, but sometimes that is a little tricky, and it is always 
>>> safe and easy to apply color in a second command, like e.g.
>>> 
>>> isosurface mysurf1 molecular;
>>> color $mysurf1 translucent green;
>>> 
>>>   
>>> --
>>> AlienVault Unified Security Management (USM) platform delivers complete
>>> security visibility with the essential security capabilities. Easily and
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>>> Jmol-users@lists.sourceforge.net
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>> 
>> 
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Re: [Jmol-users] Jmol menu surface : scripting

[Pshemak Maslak]

On 5/19/2013 12:25 PM, Otis Rothenberger wrote:

Chen,

The menu command is:

isosurface delete resolution 0 molecular map MEP translucent

This hides an important issue that I don't fully understand because of 
seemingly inconsistent charge units in various files. The issue is the 
charge range of painted colors. The above uses a default range that I 
don't know. Angel, do you know the default? By trial and error, I 
settled on the following:


isosurface resolution 0 molecular color range -.07 .07 map mep translucent


Otis



BTW: what are the units for MEP?  What is " -0.07" in the example 
above?  Is that number for potential energy?   Or just Q/distance? (Q in 
what units, distance in what units)? Or something else?


PM








--
Otis Rothenberger
o...@chemagic.com 
http://chemagic.com


On May 19, 2013, at 11:49 AM, Angel Herráez wrote:


Hello Chen

You can try enetering this in the script console just after you use 
the menu option:


show isosurface

amongst the long text displayed, there is a section entitled

which has the script that will render the isosurface you have.

As for getting a color, you can include the color definition in your 
isosurface script, but sometimes that is a little tricky, and it is 
always safe and easy to apply color in a second command, like e.g.


isosurface mysurf1 molecular;
color $mysurf1 translucent** green;

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Re: [Jmol-users] Jmol menu surface : scripting

[Otis Rothenberger]

Chen,

The menu command is:

isosurface delete resolution 0 molecular map MEP translucent

This hides an important issue that I don't fully understand because of 
seemingly inconsistent charge units in various files. The issue is the charge 
range of painted colors. The above uses a default range that I don't know. 
Angel, do you know the default? By trial and error, I settled on the following:

isosurface resolution 0 molecular color range -.07 .07 map mep translucent


Otis

--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com


On May 19, 2013, at 11:49 AM, Angel Herráez wrote:

> Hello Chen
> 
> You can try enetering this in the script console just after you use the menu 
> option:
> 
> show isosurface
> 
> amongst the long text displayed, there is a section entitled
> 
> which has the script that will render the isosurface you have.
> 
> As for getting a color, you can include the color definition in your 
> isosurface script, but sometimes that is a little tricky, and it is always 
> safe and easy to apply color in a second command, like e.g.
> 
> isosurface mysurf1 molecular;
> color $mysurf1 translucent green;
> 
>   
> --
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Re: [Jmol-users] Jmol menu surface : scripting

[Angel Herráez]

Hello Chen

You can try enetering this in the script console just after you use the menu 
option:

show isosurface

amongst the long text displayed, there is a section entitled

which has the script that will render the isosurface you have.

As for getting a color, you can include the color definition in your isosurface 
script, but sometimes that is a little tricky, and it is always safe and easy 
to 
apply color in a second command, like e.g.

isosurface mysurf1 molecular;
color $mysurf1 translucent green;


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[Jmol-users] Jmol menu surface : scripting

[陈文瀚]

Hi Bob,

I am scripting to render a molecule surface in the exactly same way as I
click the surface options in jmol menu. However, the color of the
surface(electrostatic surface) is never consistent. Is there a way to get
the command and parameters used in the menu:surface?

Cheers,


_
Wenhan Chen
School of Chemistry and Molecular Biosciences
The University of Queensland
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