RE: [PyMOL] rms

[Warren D. <wa...@de...>]

Terena,

1) verify that your selection are valid by making sure the dots appear on
the screen


select selection1, ...
select selection2, ...

2) then check to be sure that PyMOL sees matched atoms between the two
selections:

indicate selection1 in selection2
indicate selection2 in selection1

If the above commands both work, then rms_cur should output a correct value.
If they don't work, then at least one of the atomic attributes (alt, name,
resn, resi, chain, or segi) is mismatched between the two sets.  Use "alter"
to fix this, repeat step 2 to confirm success, and then reissue the rms_cur
command.
 
Cheers,
Warren

--
Warren L. DeLano, Ph.D.                     
Principal Scientist

. DeLano Scientific LLC  
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. mailto:wa...@de...      
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of Teresa
> Sent: Monday, January 10, 2005 1:58 PM
> To: pym...@li...
> Subject: [PyMOL] rms
> 
> Hi to all
> 
>  
> 
> I'm trying to use the rms_cur command and I was successful 
> when I did this:
> 
> >select selection1, (object1 and i. 57 and (name c,o,n,ca))
> 
> >select selection2, (object2 and i. 57 and (name c,o,n,ca))
> 
> >rms_cur selection1, selection2
> 
>  
> 
> but when I try to specify the chain with the residue 57 (I 
> have 6 chains in my pdb file) I got the error 
> "ExecutiveRMS-Error: No atoms selected". This is how I try:
> 
> >select selection1, (object1 and chain L and i. 57 and (name 
> c,o,n,ca))
> 
> >select selection2, (object2 and chain L and i. 57 and (name 
> c,o,n,ca))
> 
> >rms_cur selection1, selection2
> 
> I had no problems with the selection because I got the 4 
> atoms I wanted the problem was when I try to get the rms 
> between those two residues, does anybody has an idea how to 
> fix it? Am I putting the wrong syntax?
> 
>  
> 
> Thank you all for your help
> 
>  
> 
> Teresa
> 
>  
> 
> Teresa De la Mora Rey
> 
> Department of Biochemistry, Molecular Biology and Biophysics.
> 
> University of Minnesota
> 
> Lab: (612) 624-0141
> 
> "Never be afraid to try something new... remember amateurs 
> built the Ark... professionals built the 'Titanic'".
> 
>  
> 
>