[Chimera-users]

[Eric Pettersen]

On Wednesday, October 15, 2003, at 05:25 AM, solomon wrote:

> Hi,
>    I'm a new chimera user. Now I have some difficult to use chimera. 
> How can I save the amino acid that I select as a new .pdb file. For 
> example, I select the amino acids that is around the ligand within 10 
> A,and I want to save these residues as an another .pdb file. How can I 
> do?

Hi,
	There are two methods to do this.  The first involves using the 
command-line "pdbrun" command and will only work on a Unix-based system 
(i.e. any platform but Windows).  What you would do is undisplay all 
the unselected atoms (either with the command line "show sel" command, 
or via the menus by changing the Target of the Actions menu to 
"unselected atoms/bonds" and then using Actions->Atoms/Bonds->hide).  
Then you use the command line and type "pdbrun nouser cat > 
savefile.pdb" and the displayed atoms will be saved into a PDB-format 
file named "savefile.pdb".  The reason this doesn't work on Windows is 
because "cat" is a Unix command.  Another thing to consider here is 
that pdbrun saves _transformed_ coordinates (i.e. including rotations 
and translations) so if you want the coordinates to be in the same 
frame of reference as the original input coordinates, then you should 
do "reset" in the command line to get back to the original positions.
	The second method can be used on any platform but you need features 
that aren't in the 1700 release, so you would need to download the 1864 
snapshot or something newer if available.  What you do is delete all 
unselected atoms (change Actions target to "unselected atoms/bonds" and 
then Actions->Atoms/Bonds->delete).  Then you can use the command-line 
"write" command or the "write PDB" button of the model panel to write a 
PDB file (both of these save untransformed coordinates, so you don't 
need to do "reset").  Note that the deleted atoms are gone for that 
Chimera session, so if you want to get back to where you were before 
deleting them you might want to save a session before using the delete 
action.


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu
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