[chimerax-users] Analog command to reinit & create?

[Tristan Croll]

When preparing figures for a complicated structure in ChimeraX, what I found really helped was to save a session file with the model and map in a suitable starting state (i.e. with basic styles and colouring already applied) and then write the individual figure scripts to start from that point. To “reset”, just open the session file.

— Tristan

> On 13 Dec 2021, at 22:22, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Jan,
> We're glad you like ChimeraX!  Its development is an ongoing process, so if there is something you miss, you can certainly suggest it here.
> 
> I'm not a Pymol user, so bear with me if I misunderstood exactly what you wanted...
> 
> (1) There isn't a command to make absolutely everything as if you had quit and restarted, but besides "close" you could try "preset inter" and "light default""
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/preset.html>
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html>
> 
> If there are other remaining settings you may need to counteract them individually (can ask here if you're not sure what command does that).  Sometimes the lighting changes depending on the size of the structure you open, which can also cause differences.  That's called automatic styling or smart initial display and you can avoid it by using "autoStyle false" in the open command:
> <https://rbvi.ucsf.edu/chimerax/docs/user/autostyle.html>
> 
> Maybe there is Python that would do exactly what you wanted, but somebody else would have to speak to that issue.
> 
> (2)  There is a "combine" command for combining atomic models that essentially makes a new copy if you only specify one current model.
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html>
> 
> There isn't an option currently to only include part of the model, so you would then need to delete extra stuff (if any) from the copy.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> From: "Jan Gebauer" <jan.gebauer at uni-koeln.de>
>> Subject: Analog command to reinit & create?
>> Date: December 13, 2021 at 7:11:40 AM PST
>> To: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu>
>> Reply-To: "Jan Gebauer" <jan.gebauer at uni-koeln.de>
>> 
>> Hi everyone,
>> 
>> I am currently teaching a crystallographic course and this year I am introducing ChimeraX for the first time (previous years we have used PyMol).
>> I still am in the middle of my personal transiston from PyMol to ChimeraX and potentially I am still stuck too much in the "PyMol"-way to do it, but I still miss a couple of commands. Could anyone help with that?
>> 
>> 1) Analog to Reinit
>> I generate all my publication figures with scripts (now cxc). The Reinit command in Pymol, always gave me a fresh enviroment, however the closest analog I found "Close" only closes the current model. All other settings (Lightning etc.) are kept and only reset after closing ChimeraX. Therefore, I do not get the same results from my script, if I run it multiple times...
>> 
>> 2) Create object   
>> Is there a way to copy a selection of atoms into a new molecule - for complicated visualisations?
>> 
>> Thanks so far to the developers - I love more things on ChimeraX than I miss 👍
>> Best,
>> Jan
>> 
> 
> 
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