[Chimera-users] electron density in Chimera

Stefano Luciano Ciurli stefano.ciurli at unibo.it
Sat Aug 27 00:28:25 PDT 2011

Thanks a lot Terry!
I see what I can do

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 at 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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>> Chimera-users at cgl.ucsf.edu
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> -- 
> Paula Therese Lang
> Postdoctoral Scholar
> Alber Lab
> UC Berkeley/QB3
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