fetching EDS files from the web (python script)
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
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@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
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@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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participants (3)
-
Elaine Meng -
Laleh -
Tom Goddard