[chimerax-users] ChimeraX markers to IMOD model

[Tom Goddard]

Hi Joe,

  I made ChimeraX able to read IMOD model files (same as in Chimera), in the current ChimeraX daily build.  This does not help with your problem of marking particles for subtomogram averaging.  As I added IMOD model reading I looked at whether ChimeraX could write such a file.  The file has Fortran binary records and while I could write a file that ChimeraX would read, I am not sure whether IMOD or any other software would read it because the file has lots of information and I don't know what is required and what is optional.

	Tom


> On Jun 17, 2020, at 7:35 AM, Atherton, Joseph <joseph.atherton at kcl.ac.uk> wrote:
> 
> Thanks Tom
> 
> Dr Joe Atherton
> Lecturer in Cryo-electron Microscopy
> Randall Centre for Cell and Molecular Biophysics
> King's College London, UK
> Email: joseph.atherton at kcl.ac.uk <mailto:joseph.atherton at kcl.ac.uk>
> Tel: (+44) 0207 836 5454
> https://kclpure.kcl.ac.uk/portal/joseph.atherton.html <https://kclpure.kcl.ac.uk/portal/joseph.atherton.html>
> From: Tom Goddard <goddard at sonic.net>
> Sent: 16 June 2020 17:54
> To: Atherton, Joseph <joseph.atherton at kcl.ac.uk>
> Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] ChimeraX markers to IMOD model
>  
> Hi Joe,
> 
>   Neither Chimera nor ChimeraX can write IMOD model files.  (Chimera can read those files but that is not available in ChimeraX yet.)  So I don't know how you could get ChimeraX markers (which are written as an XML .cmm file) into an IMOD model.
> 
> Tom
> 
> 
>> On Jun 16, 2020, at 7:04 AM, Atherton, Joseph <joseph.atherton at kcl.ac.uk <mailto:joseph.atherton at kcl.ac.uk>> wrote:
>> 
>> Hi,
>> 
>> I'd like to use the markers function in ChimeraX to make an IMOD 'model' for use in PEET for subtomogram averaging. ChimeraX's 'planes' function makes it a convenient program for doing this. Is such an export/conversion possible?
>> 
>> All the best,
>> Joe
>> 
>> Dr Joe Atherton
>> Lecturer in Cryo-electron Microscopy
>> Randall Centre for Cell and Molecular Biophysics
>> King's College London, UK
>> Email: joseph.atherton at kcl.ac.uk <mailto:joseph.atherton at kcl.ac.uk>
>> Tel: (+44) 0207 836 5454
>> https://kclpure.kcl.ac.uk/portal/joseph.atherton.html <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fkclpure.kcl.ac.uk%2Fportal%2Fjoseph.atherton.html&data=01%7C01%7Cjoseph.atherton%40kcl.ac.uk%7Cad609f321ef94e5c329d08d81215e636%7C8370cf1416f34c16b83c724071654356%7C0&sdata=DYTk40kccjInzamJYXkJYONgX0CziJUqWyLPTkalPoU%3D&reserved=0>_______________________________________________
>> ChimeraX-users mailing list
>> ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>
>> Manage subscription:
>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimerax-users&data=01%7C01%7Cjoseph.atherton%40kcl.ac.uk%7Cad609f321ef94e5c329d08d81215e636%7C8370cf1416f34c16b83c724071654356%7C0&sdata=Qc27A%2BFjs8pozTAxmvaHYVyRonqNlMzngonQDk3n44k%3D&reserved=0>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20200617/4915c0b0/attachment.html>