input for coot
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Nurunisa Akyuz
Oct 10, 2016, 12:16:53 PM10/10/16
to EMAN2
is it possible to convert the hdf files to mtz?
Steve Ludtke
Oct 10, 2016, 1:15:29 PM10/10/16
to em...@googlegroups.com
CryoEM is not crystallography. MTZ is not really an appropriate format for CryoEM maps. Normally I believe you would use MRC/CCP4 format to get your EM maps into COOT.
On Oct 10, 2016, at 11:16 AM, Nurunisa Akyuz <nne...@gmail.com> wrote:
is it possible to convert the hdf files to mtz?
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Jason K
Oct 11, 2016, 11:30:53 AM10/11/16
to EMAN2
To get a 3D volume from hdf format into coot, use
e2proc2d.py input.hdf output.mrc
mv output.mrc output.map
coot can understand the mrc file that EMAN2 outputs, but it doesn't recognize the extension, so you have to rename it from ".mrc" to ".map"
Even though .mtz file is not really meaningful for cryoEM, when I need an .mtz file for a program that does not understand real space (such as phenix.fit_loops) then I use phenix.map_to_structure_factors in the phenix package to generate .mtz from the .map.
Jason
e2proc2d.py input.hdf output.mrc
mv output.mrc output.map
coot can understand the mrc file that EMAN2 outputs, but it doesn't recognize the extension, so you have to rename it from ".mrc" to ".map"
Even though .mtz file is not really meaningful for cryoEM, when I need an .mtz file for a program that does not understand real space (such as phenix.fit_loops) then I use phenix.map_to_structure_factors in the phenix package to generate .mtz from the .map.
Jason
Jason K
Oct 11, 2016, 11:53:26 AM10/11/16
to EMAN2
One more thing--coot is happiest when the threshold you want to use is around 1. Sometimes this isn't the case coming straight from an EMAN2 map after, say, normalize.circlemean, so when you do e2proc3d.py you should use --mult to multiply every value in the map by a scalar to bring your density down into the correct range.
If you don't do this, it'll still display OK, but when you do something like "Place Helix Here" it sometimes ends up really far away from where it was supposed to be.
If you don't do this, it'll still display OK, but when you do something like "Place Helix Here" it sometimes ends up really far away from where it was supposed to be.
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