[Chimera-users] Question about opening mrc and PDB files

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 3 14:18:27 PST 2014


Hi Min Woo Sung,
For volume measurements, see tools (both in menu under Tools… Volume Data):

Measure Volume and Area
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/measurevol/measurevol.html>

Measure and Color Blobs
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/pickblobs.html>

...and/or command "measure volume"
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#volume>

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 Feb 3, 2014, at 10:10 AM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Min Woo Sung,
> 
>  Often electron microscopy maps (.mrc file) don't have the correct grid spacing in the header.  You can tell Chimera the grid spacing in Angstroms so that the size of the map will be scaled to match PDB molecule models (which have coordinates in Angstroms).  Use the volume viewer dialog Coordinates panel (menu Features / Coordinates) and set the "voxel size" field to the distance between grid points in the map (sometimes called the "pixel size" in other software).
> 
> 	Tom
> 
> On Jan 31, 2014, at 2:18 PM, Min Woo Sung wrote:
> 
>> Hi,
>> 
>> This is Min Woo Sung from Texas A&M University.
>> I was using Chimera to see EM structure(.mrc file) and wanted to put a PDB file to fit that in EM map.
>> 
>> I'm wondering if I can use Chimera to analyze the volume, size or domains of these two files for the purpose of analysis.
>> 
>> I saw one PDB file seemed much bigger that EM map when I opened it in Chimera. Do I have to normalize the size of any files? If so, how can I do that?
>> 
>> Any suggests would greatly appreciated.
>> 
>> Best regard,
>> Min Woo Sung




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