[Chimera-users] fetching EDS files from the web (python script)

Tom Goddard goddard at sonic.net
Fri May 31 10:40:22 PDT 2013


A few more details.  In Chimera 1.7 and newer fetched files are placed in directories

	Downloads/Chimera/EDS
	Downloads/Chimera/PDB
	Downloads/Chimera/EMDB
	…

i.e. in your computer account Downloads directory there is a directory called Chimera and under that a directory for each database that Chimera has fetched files from.  Also you can fetch many files at once with the Chimera Fetch by Id dialog (File / Fetch by Id) by just entering the database identifiers as a comma separated list, e.g. 1a0m,1a2p,3gfx

As Elaine says the EDS fetch downloads brix format (".omap") so you would need a script to convert those files to MRC format.

	Tom


	
On May 31, 2013, at 10:29 AM, Elaine Meng wrote:

> Hi Laleh,
> If your preferences (Favorites… Preferences, category: Fetch) are set to save files in a download directory, they are already automatically saved locally in a subdirectory named EDS in the download directory.  However, these files are in the .omap  format, not MRC.
> 
> Since you can fetch from EDS with the "open" command and write out a map in MRC format with the "volume" command, one possibility is to make a Chimera command script.  Example commands:
> 
> open edsID:2fw0
> volume #0 save ~meng/Desktop/2fw0.mrc
> 
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output>
> 
> For combining commands with looping (for example, to process a large set of EDS IDs), see here:
> <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
> 
> 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 May 29, 2013, at 3:10 PM, Laleh <lsoltang at cs.uwaterloo.ca> wrote:
> 
>> 
>> Hello.
>> I'm wondering how I can fetch a bunch of EDS files (from the EDS server) and save them in my local machine in .mrc format. I don't want to do this manually one by one from the user interface... I tried to use open_volume_file with different settings; but it is not working... I'm surprised because this is very starightforward with pdb files. I appreciate your help.
>> Thanks in Advance,
>> Laleh
> 
> 
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