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)
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Elaine Meng
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Laleh
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Tom Goddard