[Chimera-users] saving sessions

Tom Goddard goddard at sonic.net
Wed May 8 09:50:06 PDT 2013


Hi Thomas,

  There is no session saving option that copies density map files to the same directory as the session file.  All other Chimera models including PDB files are included  (not linkied) in the session file.  The reason maps are not put into the session file is because they are sometimes very large, Gbytes in size.  Some day I intend to add an option to include the maps in the session file so you can have a self-contained session if you want. Copying the files could be another approach but it has problems.  What if there is already a map with the same file name in the current directory?  Could modify the copied file name I guess.  Maybe better put all the map files in a new subdirectory.  But are you really going to make copies of all the map files on every session save?  If you only do it sometimes it doesn't solve the problem of moving data to a new computer.  It will be slow to copy the files and it makes many redundant copies which then can become confusing as to whether two files with the same name really are identical.  Hard links could be used to avoid copying the file, but that won't work when a session is on one file system and data on another.  I think the way to handle moving data files to a new computer is to keep all your data including sessions under one directory tree so the whole thing can be easily copied.  If instead the goal is to occassionally make a self-contained session then copying the map files and session file to a new directory would be a nice option similar to embedding all files in the session.  I've noted this in the feature request for embedding the map files.

	http://plato.cgl.ucsf.edu/trac/chimera/ticket/9763

  The sphere/axes display idea is one way to see the axes of a displayed model.  The transparent sphere would cause problems in Chimera some of the time because Chimera can only correctly display one transparent model at a time.  The current default is to show a single transparent layer, so any transparent model inside the sphere would disappear.  This is a longstanding and hard problem to fix.  But a mesh could work.  Another idea is simply to depict the x,y,z axes.  I've made a feature request for this.

	http://plato.cgl.ucsf.edu/trac/chimera/ticket/12062

  Tom



On May 8, 2013, at 12:25 AM, "Marlovits,Thomas"  wrote:

> Hi Tom,
> 
> I do have a question related to saving sessions, which is a great option btw.
> Is there a way that one can save the session - let's say in a new folder but then have all models also saved in there.  For now, as I understand, it will only save the path/filename of those models.  So, whenever we switch computers, hard-drives etc … this can turn out to be a lengthy process to find those models (we often have many models open at the same time).
> Ideally, also fetched files from the pdb would be great to be saved locally in this new folder.
> 
> The second question I have is related to turning molecules around specific x/y/z angles.
> I'd love to have an option to display a big sphere that encapsulated the other models displayed.  Ideally, this sphere would look like a globe with cordinates in there … if this is displayed at semi-transparency, one can easily go to a specific position but get more of an idea to easier naviagte through the 3D space.  Sometimes I only would like to get a rough estimate about the angles to turn molecules.  Alternatively a mesh-like grid could do the same job (and if one could display the numbers of the lattidude/longitude or so that would be great too).
> 
> Many tx,
> -T.
> 
> 
> -------------------------------------------------------------------------------
> 
> Thomas C. Marlovits, PhD, M.A.S.
> The MarlovitsLab @ IMP/IMBA
> http://thomas.marlovits.myresearchlab.org
> 
> Contact/Address/Directions:
> http://thomas.marlovits.myresearchlab.org/lab/Contact.html
> 

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