Re: [Jmol-users] msg from Joel - problem converting a PyMol pse file with 'putty' display with 16.3.31

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

The script is now at JmolWiki, home page, Recycling Corner

http://wiki.jmol.org/index.php/Recycling_Corner#Rendering_protein_chain_according_to_B-factor

with some more options

________________________________
De: Angel Herraez <ang...@ua...>
Enviado: jueves, 7 de agosto de 2025 20:14
Para: Robert Hanson via Jmol-users <jmo...@li...>
Asunto: Re: [Jmol-users] msg from Joel - problem converting a PyMol pse file with 'putty' display with 16.3.31

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.
Joel, please try this

function putty(s) {
  define temp selected;
  select s and alpha;

  bMin = {selected}.temperature.min;
  bMax = {selected}.temperature.max;
  wMin = 0.2;
  wMax = 1.5;
  for (a in {selected}) {
    a.trace = wMin + (a.temperature - bMin) * (wMax - wMin) / (bMax - bMin)
  }

  set userColorScheme [xFFFFFF] [xFFE0E0] [xFFD0D0] [xFFC0C0] [xFFB0B0] [xFFA0A0] [xFF9090] [xFF8080] [xFF7070] [xFF6060] [xFF5050] [xFF4040] [xFF3030] [xFF2020] [xFF1010] [xFF0000];
  color trace property temperature "user" range @bMin @bMax;
     
  select temp;
}

and then, e.g.

putty( {*:B}  );
putty( {protein}  );




 Dr. Angel Herráez
 Biochemistry and Molecular Biology,
 Dept. of Systems Biology, University of Alcalá
 E-28805 Alcalá de Henares  (Madrid), Spain
________________________________
De: Joel Sussman <joe...@we...>
Enviado: miércoles, 6 de agosto de 2025 21:22
Para: Robert Hanson via Jmol-users <jmo...@li...>
Asunto: Re: [Jmol-users] msg from Joel - problem converting a PyMol pse file with 'putty' display with 16.3.31

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.
6-Aug-2025  22:15 Rehovot
Dear Bob
I have a problem with conversion of a PyMol pse file into a Jmol file 012_Fig_3b.pse attached.

1) for the pse: 012_Fig_3b.pse using PyMol 2_5_7 one get a nice putty view as the Cartoon - see: 012_Fig_3b_pse_PyMol_2_5_7.png

2) It looks spectacular when I drop it into Jmol 16_2_21, see:
012_Fig_3b_pse_PyMol_2_5_7_Jmol_16_2_21.png

3) But only displays wireframe in Jmol 16_3_31, see:
012_Fig_3b_pse_PyMol_2_5_7_Jmol_16_3_31.png

If you could have a look at this, and try to fix it, it would be invaluable for us at Proteopedia,
As we are using 16_3_31 in our advanced mode and would like to convert it to be the default.
Thanks
Joel

[cid:68e...@EU...]
[cid:713...@EU...]

[cid:7d9...@EU...]


--------------------------------------------------------------------------------------------
Prof. Joel L. Sussman                      Joe...@we...
Dept. of Chemical and Structural Biology   tel: +972  (8) 934 6309  www.weizmann.ac.il/~joel
Weizmann Institute of Science              fax: +972  (8) 934 6312  proteopedia.org
Rehovot 76100 ISRAEL                       mob: +972 (50) 510 9600
--------------------------------------------------------------------------------------------