Hi James.

I think it is because you create a object, which have 
identical ID's in the object.

new:
2x ID 7, 2x 5
and so on.

hide label, all
label new, index
hide label, all
label new, id

either use the index, to make selections
alter the chain name for one of the fragments, before creation

or so.

/T


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2011/12/15 James Davidson <J.Davidson@vernalis.com>
Dear All,
 
I am currently having a problem with the distance command when applied to merged objects.  The real case is actually when I remove a ligand from a binding site and merge in a new ligand.  But as a simple example, I think I can demonstrate with the following:
 
>frag ala, ala1
>frag ala, ala2
>translate [4,0,0], ala2
>label all, ID
>distance d1, ala1 & ID 3, ala2 & ID 0
 
This creates a distance object fine.  But if I now merge the two objects into a new object:
 
>create new, ala1 | ala2
>disable ala1 | ala2
 
and manually create two single atom selections corresponding to the original ID 3 and ID 0 atoms (using atom select mode and renaming the selections to give 'sele1' and 'sele2'):
 
>distance d2, sele1, sele2
 
gives me a distance between ID 0 and 3 both on what used to be ala2, and not between the two selected atoms!
 
 
Am I doing something wrong with 'create'?  I don't recall having a problem with this sort of operation until maybe ~ 6 months ago...  I am using rev 3971 under Windows.  Any help/advice greatly appreciated.
 
Kind regards
 
James

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