[Chimera-users] save map as ascii

Tom Goddard goddard at cgl.ucsf.edu
Tue Jul 21 10:23:24 PDT 2009

Hi Do-Nyun,

  The interpolate.py script on the Chimera Python scripts web page


shows how to get volume data values interpolated at specific points in a 
volume data set.  It uses trilinear interpolation from 8 nearest grid 

  More details about the volume data objects are in the Python code 
distributed with Chimera:



-------- Original Message --------
Subject: Re: [Chimera-users] save map as ascii
From: Do-Nyun Kim
To: Thomas Goddard <goddard at 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 at 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 at 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.

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