[Chimera-users] Pruning pdb graphically

[Elaine Meng]

Hi Francesco,
As usual in Chimera, there are several possible ways to do this, and  
what is "best" depends not only on what you plan to do with the  
result, but also your personal preferences and working style.

I would probably start by using either zones or Find Clashes/Contacts  
with a conservative cutoff to select all the residues you want to  
keep, which would probably also include several extra residues.  If  
you used Find Clashes/Contacts, one option selects the contacting  
atoms, and you would press the keyboard up arrow to promote the  
selection to whole residues.

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones 
 >
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html 
 >

Next, invert the selection (for example with Select... Invert (all  
models)) to include the residues you do NOT want, then undisplay them  
(for example with Actions... Atoms/Bonds... hide).

Then you can manually get rid of the few extra residues here and  
there:  Ctrl-click to select one atom or bond in an unwanted residue,  
press keyboard up arrow to promote to whole residue, undisplay as  
before.  Repeat as needed.

I don't know if you meant you wanted to just undisplay atoms or  
actually delete them.

If you wanted to delete them:  you could save PDB(s) and choose the  
option to include only the atoms that are displayed.  Alternatively,  
you could use the approach described above except instead of  
undisplaying atoms, deleting atoms (for example with Actions... Atoms/ 
Bonds... Delete) and then save PDB(s).

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#deletion 
 >
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html



On Oct 12, 2008, at 10:05 AM, Francesco Pietra wrote:

> I would like to remove several parts from a complex protein, just
> leaving the portion where a complex has been created with amberscore.
> Which is the besr way in Chimera, while observing the pruning on the
> screen?
> Thanks
> francesco pietra