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Re: [Jmol-users] msg from Joel - problem converting a PyMol pse file with 'putty' display with 16.3.31
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From: Robert H. <ha...@st...> - 2025-08-07 23:01:45
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Ah, I see. That was Angel's message. I have the PSE file. On Thu, Aug 7, 2025 at 4:58 PM Robert Hanson <ha...@st...> wrote: > Had a few minutes here so I thought I would at least look at this. > > The site you link to doesn't show the image you show here. Instead: > > [image: image.png] > > And this is exactly what I see in both versions. > > But that is not from the PSE file; that is from the PDB file with added > PyMOL-like rendering. > > Can you send me the PyMOL session file? I don't see that included in what > you sent me. > > I think what you are saying is that Jmol is not turning the putty-trace on > and instead just showing the inhibitor. Is that right? > This is quite possibly the case -- I redid the visibility settings in the > PyMOL reader and may have missed this representation. > > Bob > > > On Thu, Aug 7, 2025 at 2:45 PM Joel Sussman <joe...@we...> > wrote: > >> 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 >> <https://proteopedia.org/wiki/index.php/Sandbox_Jmol_Putty>* >> Thanks very, very much for developing this >> Best regads, >> Joel >> [image: 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...> >> *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 J*mol 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 >> >> [image: 012_Fig_3b_pse_PyMol_2_5_7_Jmol_16_3_31.png] >> [image: 012_Fig_3b_pse_PyMol_2_5_7_Jmol_16_2_21.png] >> >> [image: 012_Fig_3b_pse_PyMol_2_5_7.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 >> >> -------------------------------------------------------------------------------------------- >> >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > -- > Robert M. Hanson > Professor of Chemistry, Emeritus > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We > honor with gratitude the people who have stewarded the land throughout the > generations and their ongoing contributions to this region. We acknowledge > the ongoing injustices that we have committed against the Dakota Nation, > and we wish to interrupt this legacy, beginning with acts of healing and > honest storytelling about this place.* > -- Robert M. Hanson Professor of Chemistry, Emeritus St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place.* |
