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

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

Hello Joel
I did a little research on your file

When loaded into Jmol.jar 16.3.29, it does not display the protein, as you said.
I checked the Jmol state and indeed, it has "spacefill 0.0" for evrything and then only "wireframe" commands. No cartoon or trace.
When I load into Jmol.app 16.2.21, it looks complete and has "trace" commands after the wireframe.

If I load the state from 16.2 (copied from console) into the console of 16.3, it looks good.

So the problem, I guess, is in the PSE import into 16.3

Maybe for the moment you can save to PNGJ from 16.2 and use that for loading into Proteopedia's 16.3.

 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...]


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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
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