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

[Joel S. <joe...@we...>]

22:10 Rehovot
Dear Angel,
Just terrific(!!)
Attached is a PNGJ file you can drop into Jmol (tested on Jmol 16.3.31) to see it offline on your personal computer.
It shows the Jmol putty representation of snake toxin bound to acetylcholinesterase (1fss).
It can also be seen, interactively, on Proteopedia at:  https://proteopedia.org/wiki/index.php/Sandbox_Jmol_Putty
Thanks very, very much for developing this
Best regads,
Joel
[1fss_putty.png]
--------------------------------------------------------------------------------------------
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
--------------------------------------------------------------------------------------------

On 7 Aug 2025, at 21:49, Angel Herraez <ang...@ua...> wrote:

Caution: External Sender. Do not click on links or open attachments unless you recognize the sender.

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...<mailto:ang...@ua...>>
Enviado: jueves, 7 de agosto de 2025 20:14
Para: Robert Hanson via Jmol-users <jmo...@li...<mailto: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...<mailto:joe...@we...>>
Enviado: miércoles, 6 de agosto de 2025 21:22
Para: Robert Hanson via Jmol-users <jmo...@li...<mailto: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

[012_Fig_3b_pse_PyMol_2_5_7_Jmol_16_3_31.png]
[012_Fig_3b_pse_PyMol_2_5_7_Jmol_16_2_21.png]

[012_Fig_3b_pse_PyMol_2_5_7.png]


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

_______________________________________________
Jmol-users mailing list
Jmo...@li...<mailto:Jmo...@li...>
https://lists.sourceforge.net/lists/listinfo/jmol-users