e2pdb2mrc.py (convert pdb to mrc）

[Yaowang Li]

A 3D electron map was created from pdb file by using e2pdb2mrc.py. Then I tried convert it to IMAGIC format in em2em program, while em2em shows an error that it is a set of 2d image. could I get a single electron volume?

EMAN 2.1 alpha3 (CVS 2014/02/22 18:01:06)
Your EMAN2 is running on:  Linux-3.16.2-200.fc20.x86_64-x86_64-with-fedora-20-Heisenbug 3.16.2-200.fc20.x86_64 x86_64
Your Python version is:  2.7.3
 

[Steven Ludtke]

like any program in EMAN2, e2pdb2mrc can write any file format. The "mrc" in its name is for historical reasons. Just use an output filename with a ".hed" extension and you will get a single IMAGIC volume directly.  em2em is not reliably able to distinguish between MRC stacks and MRC volumes.

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Steven Ludtke, Ph.D.

Professor, Dept of Biochemistry and Mol. Biol.         (www.bcm.edu/biochem)

Co-Director National Center For Macromolecular Imaging        (ncmi.bcm.edu)

Co-Director CIBR Center                          (www.bcm.edu/research/cibr)

Baylor College of Medicine                             

slu...@bcm.edu

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[Yaowang Li]

Thanks very much, e2pdb2mrc.py indeed can generate the IMAGIC format file and can be read by IMAGIC.

 

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