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<div class="moz-cite-prefix">Hi Tom,<br>
<br>
on this regard I think it would be nice to have an separate
option, when saving a session, to create a self-contained session,
which would generate a directory containing the session file plus
all the data attached to that session. In this way you can take
that directory and move it elsewhere, send it to a collaborator,
etc., knowing that you can open it without scrambling for the
original data (even after years, given the great backward
compatibility of chimera). That would be also useful for archiving
purposes (often a session corresponds to a figure in a paper).
Personally I would prefer the maps out of the session files, even
if it's true that you can open the session and save the file
separately (although it's a two-step process).<br>
Just my rambling thoughts.<br>
<br>
Giovanni<br>
<br>
<br>
On 05/08/2013 09:50 AM, Tom Goddard wrote:<br>
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Hi Thomas,
<div><br>
</div>
<div> 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.</div>
<div><br>
</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span><a
moz-do-not-send="true"
href="http://plato.cgl.ucsf.edu/trac/chimera/ticket/9763">http://plato.cgl.ucsf.edu/trac/chimera/ticket/9763</a></div>
<div><br>
</div>
<div> 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.</div>
<div><br>
</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span><a
moz-do-not-send="true"
href="http://plato.cgl.ucsf.edu/trac/chimera/ticket/12062">http://plato.cgl.ucsf.edu/trac/chimera/ticket/12062</a></div>
<div><br>
</div>
<div> Tom</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div>
<div>On May 8, 2013, at 12:25 AM, "Marlovits,Thomas" wrote:</div>
<br class="Apple-interchange-newline">
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
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Hi Tom,
<div><br>
</div>
<div>I do have a question related to saving sessions,
which is a great option btw.</div>
<div>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).</div>
<div>Ideally, also fetched files from the pdb would be
great to be saved locally in this new folder.</div>
<div><br>
</div>
<div>The second question I have is related to turning
molecules around specific x/y/z angles.</div>
<div>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).</div>
<div><br>
</div>
<div>Many tx,</div>
<div>-T.</div>
<div><br>
</div>
<div><br>
<div>
<div>
<div style="font-size: 10px; ">-------------------------------------------------------------------------------</div>
<div style="font-size: 10px; "><br
class="khtml-block-placeholder">
</div>
<div style="font-size: 10px; ">Thomas C. Marlovits,
PhD, M.A.S.<br>
The MarlovitsLab @ IMP/IMBA<br>
<a moz-do-not-send="true"
href="http://thomas.marlovits.myresearchlab.org/">http://thomas.marlovits.myresearchlab.org</a><br>
<br>
Contact/Address/Directions:<br>
<a moz-do-not-send="true"
href="http://thomas.marlovits.myresearchlab.org/lab/Contact.html">http://thomas.marlovits.myresearchlab.org/lab/Contact.html</a></div>
</div>
</div>
<br>
</div>
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