Thanks a lot Terry! I see what I can do Stefano On Aug 26, 2011, at 7:27 PM, Terry Lang wrote:
Hey Stefano,
PHENIX has some problems writing maps that Chimera can successfully read. I suggest using the fft program that is distributed with the CCP4 package.
Terry
On 8/26/2011 9:29 AM, Elaine Meng wrote:
On Aug 26, 2011, at 1:24 AM, Stefano Luciano Ciurli wrote:
Hello, for a paper reporting a new structure, I would like to make a figure with Chimera, but I need a map that can be read. I have an mtz map that can be read with Coot, but I think I need to convert it to a format that Chimera can read. I cannot use the EDS server, because the file has not been released on the PDB. How do I do that? Stefano Hi Stefano, I didn't know anything about MTZ format, but found some explanation in the PHENIX mailing list that the program PHENIX can do the conversion: http://phenix-online.org/pipermail/phenixbb/2011-March/016881.html
From that message, "it's not a simple file format conversion. In this case MTZ file is supposed to contain Fourier map coefficients, and Xplor formatted file will contain Fourier image of electron density map (typically simply called "electron density map"). So this converson also involves a FT."
The PHENIX developers provide documentation and downloads for Linux and Mac. http://www.phenix-online.org/version_docs/dev-713/phenix_documentation.html
Here's a list of the density formats that Chimera "knows": http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume
Other Chimera developers or users may know more -- so it's generally better to send Chimera questions to chimera-users@cgl.ucsf.edu (which I CC'd here) instead of to me directly.
Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
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-- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3
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