Dear Chimera staff, I'm trying to get the map density data like voxel coordinates and density values at each voxel from .map files in EM database. Is there any way to get these data using Chimera? Or can I save it as an ascii file such that I can read it? All map files seem to be saved as binary files. Thank you for your consideration. Best regards, Do-Nyun Kim. -- Do-Nyun Kim, Ph.D. Laboratory for Computational Cell Biology & Biophysics Department of Biological Engineering Massachusetts Institute of Technology
Hi Do-Nyun, Chimera does not write volume data in any ascii file format. Text formats are much slower to read the files are much larger so EM maps are almost always in binary. It is not hard to read the MRC/CCP4 binary formats. Here is the specification. http://ami.scripps.edu/software/mrctools/mrc_specification.php You can use some Python code in Chimera to dump maps as text files. If there is a strong reason for doing that let me know and I'll provide some example code. Tom -------- Original Message -------- Subject: [Chimera-users] save map as ascii From: Do-Nyun Kim <kingddo@mit.edu> To: chimera-users@cgl.ucsf.edu Date: 7/20/09 1:33 PM
Dear Chimera staff,
I'm trying to get the map density data like voxel coordinates and density values at each voxel from .map files in EM database.
Is there any way to get these data using Chimera?
Or can I save it as an ascii file such that I can read it? All map files seem to be saved as binary files.
Thank you for your consideration.
Best regards, Do-Nyun Kim.
Other than writing your own script several of the em image analysis packages (e.g. spider, situs, suprim) have routines to convert between varius file formts including ASCII. The Situs package (http://situs.biomachina.org/fguide.html#map2map) uses ASCII files and has a routine to convert MRC type files to situs (map2map). Hernando Do-Nyun Kim wrote:
Dear Chimera staff,
I'm trying to get the map density data like voxel coordinates and density values at each voxel from .map files in EM database.
Is there any way to get these data using Chimera?
Or can I save it as an ascii file such that I can read it? All map files seem to be saved as binary files.
Thank you for your consideration.
Best regards, Do-Nyun Kim.
-- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa@aecom.yu.edu -----------------------------------
Hi Do-Nyun, The interpolate.py script on the Chimera Python scripts web page http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts shows how to get volume data values interpolated at specific points in a volume data set. It uses trilinear interpolation from 8 nearest grid points. More details about the volume data objects are in the Python code distributed with Chimera: chimera/share/VolumeViewer/volume.py Tom -------- Original Message -------- Subject: Re: [Chimera-users] save map as ascii From: Do-Nyun Kim To: Thomas Goddard <goddard@cgl.ucsf.edu> Date: 7/21/09 7:24 AM
Dear Tom,
Thank you for your nice reply. Can I get some example code in python? I don't need to write it down as text files, but I want to read values in density map.
Thank you for your help.
Best regards, Do-Nyun Kim.
Quoting Thomas Goddard <goddard@cgl.ucsf.edu>:
Hi Do-Nyun,
Chimera does not write volume data in any ascii file format. Text formats are much slower to read the files are much larger so EM maps are almost always in binary. It is not hard to read the MRC/CCP4 binary formats. Here is the specification.
http://ami.scripps.edu/software/mrctools/mrc_specification.php
You can use some Python code in Chimera to dump maps as text files. If there is a strong reason for doing that let me know and I'll provide some example code.
Tom
-------- Original Message -------- Subject: [Chimera-users] save map as ascii From: Do-Nyun Kim To: chimera-users@cgl.ucsf.edu Date: 7/20/09 1:33 PM
Dear Chimera staff,
I'm trying to get the map density data like voxel coordinates and density values at each voxel from .map files in EM database.
Is there any way to get these data using Chimera?
Or can I save it as an ascii file such that I can read it? All map files seem to be saved as binary files.
Thank you for your consideration.
Best regards, Do-Nyun Kim.
participants (4)
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Do-Nyun Kim -
Hernando Sosa -
Thomas Goddard -
Tom Goddard