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

--
Otis Rothenberger
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 check box lists to append and unload structures

[Angel Herráez]

Hi again

"load append" should work, but notice that once you load more than one 
model, you need ti use the "frame" or "model" command to display them. 
Also, they may be  in different coordinate systems, so one model could be 
off-screen.

I does not matter if you use checkboxes, buttons or links. All that matters is 
the JmolScript attached to them.

Try:

 jmolCheckbox("load append ''; frame all;", "zap 
file=1;"," ") ;

then you will have a way to change that "1" to different values for each 
loaded model (e.g. set a counter in your php or javascript)




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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;
>>> 
>>>   
>>> --
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>>> security visibility with the essential security capabilities. Easily and
>>> efficiently configure, manage, and operate all of your security controls
>>> from a single console and one unified framework. Download a free trial.
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>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>> 
>> 
>> 
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Re: [Jmol-users] Jmol check box lists to append and unload structures

[Manonanthini Shanmuganathan]

Hello all,
i used this script in a jmol apple to view a list of pdb structures.
jmolCheckbox("load append '';display protein;","hide
protein;"," ") ;
Even if i use this script i am not able to append multiple structures,the
only thing i can do is just loading one pdb file at a time.
I am not comfortable with javascript but i am willing to learn that
also.please guide me to proceed with appending structures with
checkbox.do i have to choose jmol button or something else.

$hit[$i] is path  to the pdb file.
$id is pdb id.

thanks and regards,
nanthini



On Sun, May 19, 2013 at 8:01 AM, Manonanthini Shanmuganathan <
manonanth...@gmail.com> wrote:

> Sirs,
> I am a research student. I am scripting a web page which has a list of pdb
> structures and a jmol window so that  we can load and unload structures but
> if I use load and load append I can view all structures at once but I am
> not able to unload and reload structures one by one using either jmol
> button or checkbox. pls help.
>
> Regards,
> Nanthini.
>
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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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> security visibility with the essential security capabilities. Easily and
> efficiently configure, manage, and operate all of your security controls
> from a single console and one unified framework. Download a free trial.
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Re: [Jmol-users] Jmol check box lists to append and unload structures

[Angel Herráez]

Hello, Nanthini

Clearing models once and again could lead you into memory use problems, 
but you can certainly try.
The command you need to clear a whole model loaded is
 zap file
 zap model

See http://www.stolaf.edu/academics/chemapps/jmol/docs/#zap

Example:
load mol1.pdb;
load append mol2.pdb;
zap file=1;  //will remove mol1.pdb





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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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