[Chimera-users] IDLE for listing selected residues.

[Eric Pettersen]

Hi JD,
	The first thing is that you probably want to refine your atom  
specifier to just select the oxygens, i.e. use:

select :HOH at o & :301.a zr < 5.0

(an extra "@o" in there).  Then use Actions...Write List to write it  
to a file.  If you really need the list in Python or need to see the  
serial numbers, then this code in IDLE would do it:

for a in chimera.selection.currentAtoms():
	print a.serialNumber

--Eric

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

On Nov 12, 2007, at 11:19 AM, Jean-Didier Maréchal wrote:


> I'd like to use chimera to generate the list of the oxygen atoms of  
> the
> water molecules located at less than 5.0 A of a ligand.
>
> Selecting the water molecules have been the easiest part...
> select :HOH & :301.a zr < 5.0
>
> with :301.a my ligand.
>
> Then in the IDLE, I tried a series of alternative to generate the  
> list.
> I use the different tips that were posted in the digest recently and
> arrived to this:
>
> for i in range(1,len(chimera.selection.currentResidues()):
> 	print chimera.selection.currentResidues()[i]
>
> Right, this gives me the list of residues, unfortunately, that  
> would be
> a LOOOT better for me is to have the Serial number of the oxygen
> atoms...
>
> currentSerialNum and currentSerialNumber do not see to be a correct
> selection type. If there is any way that can do this?