[Chimera-users] Multiple Volume Viewer Windows and saving PDB file

Thomas Goddard goddard at cgl.ucsf.edu
Tue Nov 28 12:04:20 PST 2006

Hi Batsal,

  It isn't possible to have more than one volume viewer dialog.  I
agree this would be very helpful and I've added it to my list of
projects.  There is a problem that some Chimera tools like volume
eraser or volume path tracer act on the volume shown in the unique
volume viewer dialog.  Also I'll have to think about the user
interface details of creating, hiding, and removing extra volume
viewer dialogs.

  For now one small aid to working with multiple volume data sets is
to use the volume dialog Features / Data Set List menu entry.  This
shows a list of the volume data sets and you can click on list entries
to switch between them rather than using the more cumbersome menu of
data sets.  If this is frequently useful you can use Features / Save
Default Dialog Settings so the data set list is shown by default.

  There is a bug in Chimera version 1.2304 when using menu entry File /
Save PDB....  If you have one PDB model and a map open it does not offer
you a choice of saving the PDB coordinates relative to the map.  This
is fixed in Chimera snapshot version 1.2309.  You can work around the
problem in 1.2304 by opening two PDB models.  Then Chimera will give you
the choice to save coordinates relative to the map.  The second PDB model
can be anything (another copy of the first model) and does not need to
be saved.  That's inconvenient and I recommend using Chimera 1.2309 instead.


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