Re: [Jmol-users] closed surfaces in a cluster

[Theis, K. W. <kt...@we...>]

Hi John,

The key is to give the first surface a name, and the second a different name. Otherwise, you will overwrite the first (even if you give no names at all, which is what you often see if only one surface is generated).

Less elegant than Angel's:

select O4, H5, H6
isosurface wat2 ignore {not selected} molecular translucent blue
select O1, H2, H3
isosurface wat1 ignore {not selected} molecular translucent red

[cid:6254eca7-0a72-49c2-aff2-e0d777f2855d]

You can see that the two surface overlap (because of the close approach with the hydrogen bond). Without the "ignore {not selected}" or the "only" bit, you would generate surfaces that are open at the interface.

[cid:b23ddf13-95fa-41b8-8882-784391efd3a2]


If would be nice to have a gallery of surface with the results of the rendering. I go back to the examples<https://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm>, but I think they are set up for the old Java applet, so you can't see the result of the commands (or at least I can't manage).

Karsten
________________________________
From: Angel Herraez <ang...@ua...>
Sent: Thursday, June 12, 2025 16:04
To: jmo...@li... <jmo...@li...>
Subject: Re: [Jmol-users] closed surfaces in a cluster


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Hi John
Yes indeed.
Selecting one molecule (or a part of it)  in the command itself:

isosurface w1 select (O1,H2,H3) only molecular;
color $w1 cyan translucent 0.3;
isosurface w2 select (O4,H5,H6) only molecular;
color $w2 pink translucent 0.3;

Or select beforehand  and then  use
isosurface w1 select (selected) only molecular;

 Dr. Angel Herráez
 Biochemistry and Molecular Biology,
 Dept. of Systems Biology, University of Alcalá
 E-28805 Alcalá de Henares  (Madrid), Spain

________________________________
De: John Keller via Jmol-users <jmo...@li...>
Enviado: jueves, 12 de junio de 2025 21:10
Para: Robert Hanson via Jmol-users <jmo...@li...>
Cc: John Keller <jwk...@al...>
Asunto: [Jmol-users] closed surfaces in a cluster

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.
Is it possible in Jmol to create a molecular surface around just one water in, for example, a 2-water cluster? Then, create (and display at the same time) a molecular surface around the other water molecule?
Here is the .mol file:
-----------

  WebMO

  6  4  0        0              1 V2000
    4.2162    9.0039   -0.6522 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2925    8.3928   -1.3886 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5535    9.6466   -0.8780 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4897    7.2582   -2.7834 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3570    6.3583   -2.5017 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3689    7.3270   -3.1426 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
  4  5  1  0
  4  6  1  0
M  END
------------------------------
Thanks,
John Keller
University of Alaska Fairbanks