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Feature #1877

Support reading 3d-grid data from cryo-electron microscopy tomography and X-ray crystallography

Added by Christian Blau almost 4 years ago. Updated 6 months ago.

Status:
Closed
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Normal
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Description

Comparison against experimental data within simulation or trajectory analysis requires reading from and writing to common experimental data formats.

For cryo-electron microscopy and X-ray crystallography, the common vanilla data format is the ccp4/mrc format, even though the standard slightly diverged,

I suggest implementation of the electron microscopy database (EMDB) ccp4/mrc format, documented here
ftp://ftp.wwpdb.org/pub/emdb/doc/Map-format/current/EMDB_map_format.pdf

Imlementation of other standers should be straightforward from there, if needed.

Other format specifications can be found here:
http://www.ccp4.ac.uk/html/maplib.html#description
http://www2.mrc-lmb.cam.ac.uk/research/locally-developed-software/image-processing-software/
http://bio3d.colorado.edu/imod/doc/mrc_format.txt
http://www.ccpem.ac.uk/mrc_format/mrc_format.php

The ccp4/mrc density format should also be useful for any 3d-density output, e.g. from analysis tools, since it is agnostic to the source of the data.


Related issues

Related to GROMACS - Feature #2282: Density map toolsetNew

Associated revisions

Revision c94c85dc (diff)
Added by Christian Blau 7 months ago

densityfitting - density file format (mrc) header.

Implements mrc/cc4/map format file headers as decribed in
"EMDB Map Distribution Format Description Version 1.01 (c)
emdatabank.org 2014"

Reading and writing is part of a follow-up patch.

refs #2282 and #1877

Change-Id: Ifd43cedb137c0beeb320e1299df8bae9916c8ea8

Revision 582fc1fb (diff)
Added by Mark Abraham 7 months ago

Add support for serializing 32-bit integers

Some file formats explicitly require this size, which we should
support explicitly. Note that C++ requires that int be at least 16
bits. In practice on current systems it is always 32 bits, but being
explicit might help future portability if any architecture would use
64-bit int.

Also added some support for unsigned 32- and 64-bit integers where
I saw it was missing and might be useful.

Added some test coverage where it already exists.

Refs #1877

Change-Id: I05efd7d4ba07b695fc4ed7c9d9cac8738873a3a5

History

#1 Updated by Gerrit Code Review Bot almost 4 years ago

Gerrit received a related DRAFT patchset '1' for Issue #1877.
Uploader: Christian Blau ()
Change-Id: If36bdcc4c0dbc6dee8f3455f35a6501633f90661
Gerrit URL: https://gerrit.gromacs.org/5447

#2 Updated by Christian Blau almost 2 years ago

#3 Updated by Gerrit Code Review Bot 9 months ago

Gerrit received a related patchset '1' for Issue #1877.
Uploader: Christian Blau ()
Change-Id: gromacs~master~Ia4d63faadeb595d7a2eeb4ac4760c211c0d2aac6
Gerrit URL: https://gerrit.gromacs.org/9089

#4 Updated by Gerrit Code Review Bot 8 months ago

Gerrit received a related patchset '2' for Issue #1877.
Uploader: Christian Blau ()
Change-Id: gromacs~master~Ifd43cedb137c0beeb320e1299df8bae9916c8ea8
Gerrit URL: https://gerrit.gromacs.org/9281

#5 Updated by Gerrit Code Review Bot 7 months ago

Gerrit received a related patchset '2' for Issue #1877.
Uploader: Mark Abraham ()
Change-Id: gromacs~master~I05efd7d4ba07b695fc4ed7c9d9cac8738873a3a5
Gerrit URL: https://gerrit.gromacs.org/9330

#6 Updated by Christian Blau 6 months ago

  • Status changed from New to Closed

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