converting a mrcs file to a set of png files

[ku...@healthtechnologyinnovations.com]

Hi Steve

I just downloaded EMAN2.  I am trying to convert mrcs into its constituent png files. when I used e2proc2d.  What should be the syntax I should follow? thanks in advance --kumar

[Steve Ludtke]

Hi Kumar,

e2proc2d.py --help

is always the place to start. If you do that, you'll see this example:

convert all MRC format files in current directory to HDF format:

e2proc2d.py *.mrc @.hdf

From this you can see all you need to do is:

e2proc2d.py *.mrc @.png

to convert all MRC files in the current folder to PNG format. Note that this assumes there is only one image in each MRC file. If it's an MRC stack, then you will probably want to split the MRC into multiple PNGs instead. Also note that this will produce 16 bit greyscale PNGs. If the input MRC is floating point, this may or may not be what you want, and if you are doing this for purposes of making a PPT or using photo editors, some tools may not like 16 bits.

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)
Co-Director National Center For Macromolecular Imaging                  (ncmi.bcm.edu)

On Nov 20, 2018, at 5:05 PM, ku...@healthtechnologyinnovations.com wrote:

Hi Steve

I just downloaded EMAN2.  I am trying to convert mrcs into its constituent png files. when I used e2proc2d.  What should be the syntax I should follow? thanks in advance --kumar

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[ku...@healthtechnologyinnovations.com]

Thanks Steve.  I looked thru the spec (provided by help), and did the following, and it worked:

e2proc2d.py classes.mrcs class.png --unstacking

This produced class-001.png thru class-100.png (100 class images stored in the mrcs file), which is what I was looking to create. However, I think the png images are not sharp (somewhat fuzzy).  Is there any flag/parameter that I could set to "sharpen" images?

Regards

--kumar