[Chimera-users] Saving sessions including maps?

[Oliver Clarke]

Ok, so if I run the following python script at chimera startup (to add a mkdir command):

def mkdir(mkdir,dir1):
  import os
  import time
  if not os.path.exists(dir1):
    os.mkdir(dir1)
from Midas.midas_text import addCommand
addCommand("mkdir", mkdir, help=False)

And then add the following alias:

#Save session with maps. saves in home dir with directory name same as session.
# Usage: save_session_dir session-name
# Don't use spaces or under_scores in session names.
alias ^save_session_dir  cd ~; mkdir $1; volume # save ~/$1/$1%d.mrc; save ~/$1/$1

This seems to work okay. It will create a sub dir in the user’s home directory with maps and a chimera session file.

Incidentally, is there any easy way to add python code snippets to a Chimera command file (with aliases etc)? I guess the only ways are to either have it in a separate file and use open or runscript, or to make it one big python file and wrap all of the aliases in runcommand() calls. But then how does one tell Chimera to run a given python file at start up? When I add python files to the “Files to read at startup” section of preferences, Chimera seems to interpret them as Chimera command files, and hence gives an error.

Cheers,
Oliver.
> On Sep 11, 2015, at 9:04 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Thanks for the quick reply Tom, got it. Looking forward to Chimera 2!
> 
> One temporary work around I have thought about is the following alias:
> 
> #Save session with maps. saves in home dir with directory name same as session.
> # Usage: save_session_dir session-name
> # Don't use spaces or under_scores in session names.
> alias ^save_session_dir volume # save ~/$1/map%d.mrc; save ~/$1/$1
> 
> This will save all maps in a subdir of the home directory with the desired session name, and then save the session in the same dir - this folder is then portable and has all the info needed to restore the session. The only caveat to this is that this only works if the directory already exists - otherwise it gives an error. Maybe it would be possible to add an option to save/write to make the dir if it does not already exist? Otherwise I can do it in python I guess. Also, map names are not preserved, but I don’t see any easy way to get around that. Only other problem with this is that because of the way aliases work in chimera, any underscores in the alias arguments will be converted to spaces, but that is not an issue so long as one is aware of it.
> 
> Cheers,
> Oliver.
>> On Sep 11, 2015, at 6:54 PM, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>> 
>> Hi Oliver,
>> 
>>   This has long been a requested feature.
>> 
>> 	http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426>
>> 
>> And I agree it would be useful.  If Chimera packages up all the needed maps and the session file in a zip archive this would be convenient.  You can of course do this right now by hand, only it isn’t so convenient.  Unfortunately this has never reached a high enough priority relative to other enhancements we are working on, so it has not been implemented.  It is more likely to get into Chimera 2 than Chimera 1.
>> 
>> 	Tom
>> 
>> 
>>> On Sep 11, 2015, at 2:05 AM, Oliver Clarke wrote:
>>> 
>>> Hi all,
>>> 
>>> Is there any possibility of altering the chimera session format (or adding a separate option) such that all maps (including those created during the session) are also saved? 
>>> 
>>> This would greatly facilitate sharing data with collaborators, and would also allow one to provide chimera sessions with saved scenes as supplementary data when publishing.
>>> 
>>> It would also make saving sessions more practical when many different volumes are created during the session - for example, when using a molmap low resolution representation for each domain.
>>> 
>>> This would not necessarily require creating a new format - just creating a tarball or folder with all the maps and relative paths specified in the python file would work fine I think?
>>> 
>>> Cheers,
>>> Oli.
>>> 
>>> 
>>> 
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>>> 
>> 
> 

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