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

Oliver Clarke olibclarke at gmail.com
Thu Sep 24 14:00:27 PDT 2015


Aha, great. Thanks Eric!’

Oliver.
> On Sep 24, 2015, at 4:58 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> 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.
> 
> —Eric
> 
>> 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)
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
> 




More information about the Chimera-users mailing list