technical questions about volume viewer in chimera
Hallo Perhaps, this has been on the forum before, but I could not find the answers to my questions: 1. Some EM density maps have a header. I wonder how Chimera recognizes it and calculates map dimensions? 2. Does chimera take default voxel size from header of EM file? Thanks in advance Alex ---------------------------------------------------------------------- Alexander Shkumatov, predoc -- Biological Small Angle Scattering Group EMBL Hamburg Outstation c/o DESY -- Building 25A Notkestraße 85 -- 22603 Hamburg -- Germany tel: +49 40 89902 178 fax: +49 40 89902 149 Email: shkumatau@embl-hamburg.de ----------------------------------------------------------------------
Hi Alex, The header is read from at least some formats to set the map origin and voxel size. Tom G, our expert on this subject, is away until after Sept 10, but perhaps these previous posts will answer your questions: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-September/000961.html> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-September/000964.html> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-September/000965.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 1, 2010, at 4:31 AM, Alex Shkumatov wrote:
Hallo Perhaps, this has been on the forum before, but I could not find the answers to my questions: 1. Some EM density maps have a header. I wonder how Chimera recognizes it and calculates map dimensions? 2. Does chimera take default voxel size from header of EM file? Thanks in advance Alex
Hi Alex, Chimera reads the voxel size and map grid size from the headers of each of the volume file formats it reads. Often the correct voxel size is not given in the files and is set to 1.0. If it the file has zero (or negative) for the voxel size than Chimera uses of size of 1. You can change the voxel size within Chimera using the volume dialog Coordinates panel. Then you can save a new file with the volume dialog File / Save Map As... menu entry. Tom
Hallo
Perhaps, this has been on the forum before, but I could not find the answers to my questions: 1. Some EM density maps have a header. I wonder how Chimera recognizes it and calculates map dimensions? 2. Does chimera take default voxel size from header of EM file?
Thanks in advance Alex
Hi Tom, Elaine Thanks for your replies - very helpful! I followed one of the links from Elaine's email: http://ami.scripps.edu/prtl_data/mrc_specification.htm Does this actually mean that pixel size is not provided in MRC file? Could you also perhaps comment on how chimera recognizes the density files with inverted order of bytes? Thanks in advance Alex Quoting "Tom Goddard" <goddard@sonic.net>:
Hi Alex,
Chimera reads the voxel size and map grid size from the headers of each of the volume file formats it reads. Often the correct voxel size is not given in the files and is set to 1.0. If it the file has zero (or negative) for the voxel size than Chimera uses of size of 1. You can change the voxel size within Chimera using the volume dialog Coordinates panel. Then you can save a new file with the volume dialog File / Save Map As... menu entry.
Tom
Hallo
Perhaps, this has been on the forum before, but I could not find the answers to my questions: 1. Some EM density maps have a header. I wonder how Chimera recognizes it and calculates map dimensions? 2. Does chimera take default voxel size from header of EM file?
Thanks in advance Alex
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
---------------------------------------------------------------------- Alexander Shkumatov, predoc -- Biological Small Angle Scattering Group EMBL Hamburg Outstation c/o DESY -- Building 25A Notkestraße 85 -- 22603 Hamburg -- Germany tel: +49 40 89902 178 fax: +49 40 89902 149 Email: shkumatau@embl-hamburg.de ----------------------------------------------------------------------
Hi Alex, The pixel size is in the MRC file header. It is (CELLA[0]/mx, CELLA[1]/my, CELLA[2]/mz). Refer to the MRC file documentation for details. http://www2.mrc-lmb.cam.ac.uk/image2000.html There is a file header word MACHST used to distinguish big-endian from little-endian files (value 0x11 0x11 0x00 0x00 or 0x44 0x44 0x00 0x00). Chimera does not use that. I think the reason is that it is not always set. In fact Chimera did not set it correctly when writing MRC files until just yesterday. Instead Chimera looks at the number of map columns (NC) and chooses the byte order that makes that value between 1 and 65536. For more details of reading MRC files see the Chimera python code in your distribution chimera/share/VolumeData/mrc/mrc_format.py On Mac the share directory is Chimera.app/Contents/Resources/share. Tom
Hi Tom, Elaine
Thanks for your replies - very helpful!
I followed one of the links from Elaine's email: http://ami.scripps.edu/prtl_data/mrc_specification.htm
Does this actually mean that pixel size is not provided in MRC file? Could you also perhaps comment on how chimera recognizes the density files with inverted order of bytes?
Thanks in advance Alex
Quoting "Tom Goddard" <goddard@sonic.net>:
Hi Alex,
Chimera reads the voxel size and map grid size from the headers of each of the volume file formats it reads. Often the correct voxel size is not given in the files and is set to 1.0. If it the file has zero (or negative) for the voxel size than Chimera uses of size of 1. You can change the voxel size within Chimera using the volume dialog Coordinates panel. Then you can save a new file with the volume dialog File / Save Map As... menu entry.
Tom
Hallo
Perhaps, this has been on the forum before, but I could not find the answers to my questions: 1. Some EM density maps have a header. I wonder how Chimera recognizes it and calculates map dimensions? 2. Does chimera take default voxel size from header of EM file?
Thanks in advance Alex
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
---------------------------------------------------------------------- Alexander Shkumatov, predoc -- Biological Small Angle Scattering Group EMBL Hamburg Outstation c/o DESY -- Building 25A Notkestraße 85 -- 22603 Hamburg -- Germany
tel: +49 40 89902 178 fax: +49 40 89902 149 Email: shkumatau@embl-hamburg.de ----------------------------------------------------------------------
participants (3)
-
Alex Shkumatov -
Elaine Meng -
Tom Goddard