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

[Angel H. <ang...@ua...>]

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