[Chimera-users] Way to extract path to file from model ID

Eric Pettersen pett at cgl.ucsf.edu
Thu Sep 24 13:58:45 PDT 2015

If a model has an “openedAs” attribute (which I believe all models opened from files have), then openedAs[0] is the path of the input file.


> On Sep 24, 2015, at 1:39 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> Hi all, I’m wondering, is there any way (presumably via a python function) to get the path to the original file from the model ID?
> I’ve written a little python jiffy (below) so I can lowpass filter maps to a specified resolution on the fly inside chimera using EMAN, but is quite slow because I need to first write a copy of the map out (so I know where it is) and then modify it. If anyone knows of an easier way to do such things I would be most grateful.
> Cheers,
> Oli.
> Script:
> def cmd_lowpass(lowpass,args):
>  from Midas.midas_text import doExtensionFunc
>  def lowpass(model,resol):
>    import os
>    from chimera import runCommand
>    import subprocess
>    import sys
>    #You may need to change the below to .bash_profile if on mac.
>    #You must have EMAN2 in your bash path for this to work correctly.
>    #If running multiple times, you need to close the first instance of lowpass.mrc before creating a second.
>    bashrc_path=os.path.expanduser("~/.bashrc")
>    freq=1.0/resol
>    command="cd ~; system mkdir chimera_tmp; cd chimera_tmp; volume "+model+" save ./tmp1.mrc"
>    runCommand(command)
>    pathvar=os.path.expanduser("~/chimera_tmp")
>    os.chdir(pathvar)
>    e2string="--process=filter.lowpass.gauss:cutoff_freq="+str(freq)
>    print(e2string)
>    mrc_in=pathvar+"/tmp1.mrc"
>    mrc_out=pathvar+"/lowpass.mrc"
>    e2command="source "+bashrc_path+"; bash -c \"e2proc3d.py"+" "+mrc_in+" "+mrc_out+" "+e2string+"\""
>    print(e2command)
>    proc=subprocess.Popen(e2command,stdout=subprocess.PIPE, stderr=subprocess.PIPE,shell=True)
>    out, err = proc.communicate()
>    print 'stdout:', out
>    print 'stderr:', err
>    runCommand("open lowpass.mrc")
>  doExtensionFunc(lowpass,args)
> from Midas.midas_text import addCommand
> addCommand("lowpass", cmd_lowpass, help=False)
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