Thanks for that one; it works as advertised.

Another question: if I have 10 different structures read into PyMOL, what is the best (most accurate) method for aligning the structures as an ensemble? Currently, I'm aligning all to the first structure read in (i.e. 2>1, 3>1, etc.) using a for loop and the 'align' command. Since the structures have different sequences, I cannot use 'intra_fit', etc., is that right? Are there any other commands or methods of aligning that might be easy to script?

Thanks,
Doug


On Jan 20, 2005, at 2:12 PM, Warren DeLano wrote:

Doug,

Setwise logical ANDs and ORs are tricky at first. In this case, you want to create a new set that contains atoms in a1 *or* a2. There aren't any atoms
that are in both a1 and a2 which is why you're ending up with an empty
object.

create one, a1 or a2

-----Original Message-----
I'm having some problems with selection syntax w/ multiple objects.
I've loaded four different PDB files (in sequence & structure):

    load 1.pdb, a1
    load 2.pdb, a2
    load 3.pdb, b1
    load 4.pdb, b2

I wanted to create two new selections:

    one = a1 & a2
    two = b1 & b2

I've tried many different combinations of PyMOL selection
syntax, but I cannot get the objects to add to the same
selection (using 'create' or
'select'):

    create one, a1 + a2
    create one, a1 and a2
    create one, object a1 + object a2
    create one, a*

 From what I've read in the manual, I think these commands
are not working because they actually work to select atoms
that are the same between a1 & a2.  The manual says it
'selects atoms included in both s1 and s2'.

Any clues or hints?

Thanks,
Doug



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