Re: [Jmol-users] msg from Joel - PyMOL "pse" file to Jmol probelms

[Robert H. <ha...@st...>]

https://sourceforge.net/projects/jmol/files/Jmol/Version%2016.3/Jmol%2016.3.15/

I may not have tested everything you sent me, Joel, but I think I covered
most of the issues.

Backgrounds are a bit tricky, as the default PyMOL background is "none".
This is recreated using WRITE xxxx.png as PNGT

So do let me know what I missed. I'm certainly interested in more
development on this. We will never fully reproduce all that PyMOL can
produce, but we can come close. I did some major reworking of the settings
logic, and so what's left may not be too hard to add.

This 013_Fig_2c.pse was not one I used for testing. Now showing the
following, which I think looks better than the PyMOL version, actually.

[image: image.png]







On Sun, Apr 6, 2025 at 1:27 AM Joel Sussman <joe...@we...>
wrote:

> 6 Apr 2025 09:20 Rehovot
> Dear Bob
> I have a problem with conversion of PyMol (*.pse) to Jmol.
> When I try to use PyMol version 2.6.0 and write a 'pse' file for it:
>
> 1) Jmol 14.31.8 works just fine but does not keep the WHITE Background
> 2) Jmol 16.2.1 and 16.3.11 keep WHITE background but only shows
> spheres (spacefil) for the metal ions, and not for the atoms in organic
> residues.
>
> see
> text of the PyMol file:   013_FIg_2c and 013_Fig_2.pse
> screenshots of output for PyMol and, Jmol 14/31.8, 16.2.1, 163.11
>
> If you can try to solve this, it would be great
> thanks
> Joel
>
> ---------------------------------------------------------------------------------------------
> 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
>
> ---------------------------------------------------------------------------------------------
>
>
>
>
>

-- 
Robert M. Hanson
Professor of Chemistry, Emeritus
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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