Re: [Jmol-users] isosurface question

[Daniel F. <fen...@ml...>]

This worked well.  I then followed up with
 isosurface color translucent
to show why the regions are hydrophobic

Thanks again!

On Fri, Aug 29, 2025 at 2:05 PM Daniel Fenske <fen...@ml...> wrote:

> Thanks!  Could not figure out what to do about the error!
>
> On Fri, Aug 29, 2025 at 9:47 AM Angel Herraez <ang...@ua...>
> wrote:
>
>> Hey! Maybe this
>> isosurface solvent map mep 3
>>
>> "3" = e^(-d)
>>
>> *Fauchere, J. L.; Quarendon, P.; Kaetterer, L. Estimating and
>> representing hydrophobicity potential. J. Mol. Graphics 1988, 6, 203-206.*
>>
>> or
>> isosurface solvent map mep 1
>>
>> "2" = 1/(1+d)
>> *Audry, E.; Dubost, J. P.; Colleter, J. C.; Dallet, P. A new approach to
>> structure-activity relations: the "molecular lipophilicity potential". Eur.
>> J. Med. Chem. 1986, 21, 71-72*
>>
>>  Dr. Angel Herráez
>>  Biochemistry and Molecular Biology,
>>  Dept. of Systems Biology, University of Alcalá
>>  E-28805 Alcalá de Henares  (Madrid), Spain
>> ------------------------------
>> *De:* Angel Herraez <ang...@ua...>
>> *Enviado:* viernes, 29 de agosto de 2025 16:35
>> *Para:* Jmo...@li... <
>> Jmo...@li...>
>> *Asunto:* Re: [Jmol-users] isosurface question
>>
>> *ATENCIÓN*: Este correo electrónico se envió desde fuera de la UAH. No
>> haga clic en enlaces ni abra archivos adjuntos a menos que reconozca al
>> remitente y sepa que el contenido es seguro.
>> Hello Dan
>> That way can only be used with solid colors. You will need color mapping,
>> something like MAP MEP or MAP property.
>> I cannot give exact details, but see this:
>> https://chemapps.stolaf.edu/jmol/docs/#isosurfacemapcolormappingdataset
>>
>>
>>
>>
>>  Dr. Angel Herráez
>>  Biochemistry and Molecular Biology,
>>  Dept. of Systems Biology, University of Alcalá
>>  E-28805 Alcalá de Henares  (Madrid), Spain
>> ------------------------------
>> *De:* Daniel Fenske <fen...@ml...>
>> *Enviado:* viernes, 29 de agosto de 2025 14:38
>> *Para:* Jmo...@li... <
>> Jmo...@li...>
>> *Asunto:* [Jmol-users] isosurface question
>>
>> *ATENCIÓN*: Este correo electrónico se envió desde fuera de la UAH. No
>> haga clic en enlaces ni abra archivos adjuntos a menos que reconozca al
>> remitente y sepa que el contenido es seguro.
>> Hello,
>> I have looked at the wikis and let AI chew on this for me, to no avail.
>> I want to display a simple sucrose molecule (got that) and show its
>> hydrophobic/hydrophilic properties.
>> I used the command
>>
>> isoSurface solvent
>>
>> to generate the isosurface.  All good.  I can use the command
>>
>> color isoSurface red (or another defined color)
>>
>> to give it color.
>>
>> The instructions I have found say that the following command should color
>> the surface according to hydrophobicity
>>
>> color isoSurface hydrophobicity
>>
>> but jmol gives the error
>>
>> script ERROR: bad argument count
>>
>> Can someone point me in the right direction?  Many thanks!
>>
>>
>> --
>> Prof. Dan Fenske
>>
>> Job 42 Then Job replied to the Lord: “I know that you can do all things; no
>> purpose of yours can be thwarted.
>>
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>
>
> --
> Prof. Dan Fenske
>
> Job 42 Then Job replied to the Lord: “I know that you can do all things; no
> purpose of yours can be thwarted.
>


-- 
Prof. Dan Fenske

Job 42 Then Job replied to the Lord: “I know that you can do all things; no
purpose of yours can be thwarted.

-- 
This electronic communication, including any attached 
documents, may 
contain confidential and/or legally privileged 
information that is 
intended only for use by the recipient(s) named 
above. If you have 
received this communication in error, please notify 
the sender immediately 
and delete the communication and any 
attachments. Views expressed by the 
author do not necessarily represent 
those of Martin Luther College.