[PyMOL] export 2 molecules to one pdb file?

2008-08-13 Thread Paul Shannon 
Thanks to Warren for setting me straight on independent positioning of  
molecules.


Now I wish to write out the two molecules, together, to one pdb file,
as required by RosettaDock.  I must be blind.  They say:

   ...from the main menu, File→Export Molecule can be used to write  
a PDB file containing

   the starting structure with both docking partners.

The closest menu option I can find (using MacPyMol) is File-Save  
Molecule...

The resulting dialog apparently only allows one object to be written.

Any advice?  Thanks!

 - Paul

Re: [PyMOL] export 2 molecules to one pdb file?

2008-08-13 Thread Nathaniel Echols 
Just use the (PyMOL) command line: save complex.pdb will save all objects.
 You'll need to figure out what directory you're in first - by default, this
is probably /Applications, but cd ~ will get you home.  (Hey Warren, could
this be changed so cd alone works, like in a Unix shell?)
(Or if you have more than just those two molecules: save complex.pdb,
object1 or object2)

On Wed, Aug 13, 2008 at 12:01 PM, Paul Shannon
pshan...@systemsbiology.orgwrote:

 Thanks to Warren for setting me straight on independent positioning of
 molecules.

 Now I wish to write out the two molecules, together, to one pdb file,
 as required by RosettaDock.  I must be blind.  They say:

...from the main menu, File→Export Molecule can be used to write
 a PDB file containing
the starting structure with both docking partners.

 The closest menu option I can find (using MacPyMol) is File-Save
 Molecule...
 The resulting dialog apparently only allows one object to be written.

 Any advice?  Thanks!

  - Paul
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[PyMOL] map outside the unit cell

2008-08-13 Thread Rahul Shanmugasundararaj 
Hi, 
I created the ccp4 format  map files in Coot from mtz. Pymol displays the map 
only for residues within the unit cell. How do I display the map outside the 
unit cell.
Any suggestions?
Thanks
Rahul