[Chimera-users] Matlab script for reading volume data

[Thomas Goddard]

Hi Do-Nyun,

   The matlab script on the MRC file format specification web page at

	http://ami.scripps.edu/software/mrctools/mrc_specification.php

was not written by us.  But that appears not to be the script you are 
referring to since it merely reads MRC grid size and data values and 
does not read the origin, cell size, or cell angles.

   The Chimera code that reads an MRC map is in Python and included in 
the distributions:

    chimera/share/VolumeData/mrc/mrc_format.py

It uses other Chimera modules (Matrix and VolumeData) so it can't be 
used on its own.

	Tom


-------- Original Message --------
Subject: Re: [Chimera-users] save map as ascii
From: Do-Nyun Kim
To: Tom Goddard
Date: 7/23/09 8:22 AM

> Dear Tom,
> 
> It seems Voxel information in Volume Viewer is different from that by reading
> .mrc map data.
> 
> For example,
>  I opened "emd_1080.map" and saved it as "emd_1080.mrc".
> 
> In volume viewer,
>   Origin index = 50, Voxel size = 2.7, Cell angles = 90.
> 
> But if I use matlab script you linked,
>   Origin = -1022951423, Cell size = 1132920833, Cell angle = 1119092736
> 
> Could you let me know how to convert values from .mrc data to those shown in
> volume viewer?
> 
> Thank you.
> 
> Best regards,
> Do-Nyun Kim.
> 
>> -------- Original Message --------
>> Subject: Re: [Chimera-users] save map as ascii
>> From: Do-Nyun Kim
>> To: Thomas Goddard 
>> 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.
>>>>>