[chimerax-users] Trying to open .py files on Windows gives cPickle error

[Elaine Meng]

Great!!!  I'm glad it worked for your data! 

Nowadays I'd rather work with ChimeraX than Chimera, so I've used the export a few times myself...

Best,
Elaine

> On Aug 9, 2021, at 5:55 PM, Carnes, Jason via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Elaine,
> 
> Thank you so much for that Chimera export help! That has solved the problem entirely. I truly appreciate you taking the time to guide us through it.
> 
> Cheers,
> 
> Jason
> 
> -----Original Message-----
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Monday, August 9, 2021 5:32 PM
> To: Carnes, Jason <Jason.Carnes at seattlechildrens.org>
> Cc: ChimeraX Users Help <ChimeraX-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] Trying to open .py files on Windows gives cPickle error
> 
> CAUTION: This email originated outside of this organization.
> 
> Hi Jason,
> Well, the simplest and most foolproof solution if they saved a Chimera session (.py file from Chimera menu:File... Save Session, or Chimera's "save" command) is for you to use Chimera to open it, not ChimeraX!
> 
> However, the export to ChimeraX of which I speak is Chimera menu: File... Export Scene, or "export" command.  Then they would have to choose or specify the format option : ChimeraX
> 
> Here's the Chimera help for Export Scene:
> <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html__;!!NuzbfyPwt6ZyPHQ!5sncYicZMg-r5mtKFMvHWYv1w_ZWXe4LMmopGUXCdHrrn1N7dnBxsRHsGhuWR8alHEEU_18hIg$ >
> 
> If they used this exporting mechanism to save a .py file from Chimera, then you should be able to open it in ChimeraX without error.  However,  this export does not include every possible thing yet like density maps.  If you are working only with atomic structures, however, it may fill the bill.
> 
> I hope this helps,
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On Aug 9, 2021, at 5:24 PM, Carnes, Jason via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> Elaine,
>> 
>> You are correct that my friend is using Chimera (not ChimeraX). We were a bit confused in our communication on that point.
>> 
>> They can save to a .pdb file, but that file erases all of the color highlighting and hidden parts of the structure that is the reason why we want to share files in the first place.
>> 
>> Can you elaborate on the method to save from Chimera (or export?) in a format that ChimeraX recognizes? I am running ChimeraX and can't see their menu structure.
>> 
>> Thanks so much for your quick reply!!!
>> 
>> Jason
>> 
>> 
>> -----Original Message-----
>> From: Elaine Meng <meng at cgl.ucsf.edu>
>> Sent: Monday, August 9, 2021 4:30 PM
>> To: Carnes, Jason <Jason.Carnes at seattlechildrens.org>
>> Cc: chimerax-users at cgl.ucsf.edu
>> Subject: Re: [chimerax-users] Trying to open .py files on Windows
>> gives cPickle error
>> 
>> CAUTION: This email originated outside of this organization.
>> 
>> Hi Jason,
>> I am mystified by "their only option to save modified files"... if you mean a modified atomic structure, ChimeraX can write .pdb and .cif (mmCIF), as well as save ChimeraX session files (.cxs).  These can be done with the "save" command or menu: File... Save and choosing file type in the dialog.
>> 
>> Maybe that person is using Chimera instead and is saving a Chimera session file (.py) but they would also have the option of writing a PDB file from Chimera, if it is an atomic structure.
>> 
>> In other words, I don't understand why somebody is saying that their only option to save modified files is python, especially if they are really using ChimeraX rather than Chimera!  So there shouldn't be any reason why you need to open their python file in ChimeraX.  If they are really using Chimera, there is an option to export to ChimeraX that provides a python file, but your opening such a file in ChimeraX should not give that error.  As far as I know, this has nothing to do with Mac vs. PC.
>> 
>> Best,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry University of California, San
>> Francisco
>> 
>>> On Aug 9, 2021, at 4:14 PM, Carnes, Jason via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>> 
>>> Hello,
>>> I am collaborating with someone using ChimeraX on a Mac. Their only option to save modified files results in a .py file extension. When I try to open .py files on my Windows install of ChimeraX I get an error:
>>> 
>>> “ModuleNotFoundError: No module named 'cPickle'”
>>> 
>>> Is there a way to manually install cPickle on my Windows computer that will allow me to open the .py files, or are Mac & PC not compatible?
>>> Thanks,
>>> Jason
>> 
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