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The MRC format historically had no internal mechanism for distinguishing between 2D stacks and 3D volumes. The current version (EMAN2.12) will distinguish between the two based on filename. Files with .mrcs extension will be treated as stack files, and files with any other extension interpreted as MRC will be treated as 3D (if they are volumes). The trick you used with --threed2twod will also work, but is no longer the preferred mechanism.  ".mrcs" files can be used as a 2-D stack with any EMAN2 program, not just e2proc2d.
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Steven Ludtke, Ph.D.
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On Nov 10, 2015, at 4:21 PM, Liz Montabana <[log in to unmask]> wrote:

I don't know if this is what is supposed to happen, but when using relion_stack_create, the output I get is read into other programs (like eman1.9 and eman2) as a 3D volume rather than a stack of 2D slices. I just used e2proc2d.py with the "--threed2twod" option to covert to a stack of 2D slices.

Cheers
Liz Montabana

On Tue, Nov 10, 2015 at 1:30 PM, Joshua Lobo <[log in to unmask]> wrote:
Thank you Ludovic and Oliver

I will try both of your suggestions . is Relion_stack_create meant to run in paralell or on a single processor.?Is there a resource for the more advanced scripts in Relion like relion_stack_create which I can read up on so
that i can make a better decision as which script to use when?



On Tue, Nov 10, 2015 at 9:35 AM, Oliver Clarke <[log in to unmask]> wrote:
However, with a lot of particles you may run out of memory - relion_preprocess --operate_on in.star --o out_rootname seems to work more reliably in such instances.

Cheers,
Oliver.

On Tue, Nov 10, 2015 at 9:30 AM, Ludovic Renault <[log in to unmask]> wrote:
Hi,

relion_stack_create works on star files and output an mrcs file (that you can then convert with any other program if needed).
So if you saved a 2d cleaned star file after 2d cl then you can create a mrcs stack from this yes.

Ludo

On Tue, Nov 10, 2015 at 2:14 PM, Joshua Lobo <[log in to unmask]> wrote:
Hi Everyone


I was wondering if there was any way to create a stack out of all the autopicked particles from a star file . The final extraction step after autopick creates a star file .Could I run a 2D classification on this star file and then use the relion_stack_create to stack the mrc files . If there is a different way of doing this or a fault in this methodology I would like to know . Relion stack create looks for .mrcs to stack them up,

Any suggestions are welcome

Sincerely
Joshua Lobo





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Joshua Lobo
Biomedical Engineering 
Virginia Commonwealth University