[Chimera-users] Writing the selection

Charles Moad cmoad at indiana.edu
Tue Apr 19 12:10:02 PDT 2005

I don't need coords, just knowledge of which residues are selected,
hence writesel should suffice.

Thanks as always,

Elaine Meng wrote:
> On Tuesday, April 19, 2005, at 11:34 AM, Charles Moad wrote:
>> How can I write the current selection to a file from a script?
>> "write sel filename.pdb" does not work.
> Hi Charlie,
> Did you need the coordinates, or a text description of the
> selection?  A parseable text description of the selection can
> be written to a file with
>   Actions... Write
> or the command writesel (new in the March snapshot, 1.2105).
> The man page can be viewed at
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/writesel.html
> As for the coordinates, we do not currently have a general way
> of writing them out for just the selection (but it's on the "to do"
> list).  However, if you are on a UNIX system, you can save the
> coordinates of the selection using the following procedure.
> Chimera can send information on what atoms are displayed to the
> system, and then the system command "cat" can send the information
> to a file.  In Chimera, if the atoms of interest are selected:
>      show sel
>      pdbrun nouser cat > ~homedir/myfile.pdb
> (where "homedir" is your username) saves the displayed atoms to a PDB
> file named myfile.pdb in your home directory.  It is necessary to use
> show (which undisplays everything else) since pdbrun includes all atoms
> that are displayed.  The coordinates are transformed, so will be different
> from the original coordinates if you have moved the view around.  If you
> want the untransformed coords, use the "reset" command before the "pdbrun"
> command. This process doesn't work on Windows as there is no cat command.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                      http://www.cgl.ucsf.edu/home/meng/index.html

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