I'm working on a script which involves joining two objects together, which
I do using the create command. The input objects have different chain
identifiers, but identical residue numbers. When I create the joined
object, I would expect all atoms from the first object to be added,
followed by all atoms from the second object (with atom IDs being unchanged
for the first object, and then continuing sequentially for the second
object). Instead, the produced object alternates between atoms of each of
the input objects:
PyMOL>iterate joined, print (ID,chain,name)
(0, 'A', 'N')
(1, 'B', 'N')
(2, 'A', 'CA')
(3, 'B', 'CA')
(4, 'A', 'C')
(5, 'B', 'C')
(6, 'A', 'O')
(7, 'B', 'O')
...
This order breaks cartoon and ribbon representations, as well as makes the
sequence view display each atom individually rather than combining residues.
A somewhat convoluted but reproducible case follows (Using MacPyMOL 1.7.4):
fetch 4rp9, type=pdb1
split_states 4rp9
alter 4rp9_0002, chain = 'B'
create joined, 4rp9_* and resi 282
I've tried various combinations of the rebuild and sort commands, as well
as manually changing the IDs of the objects, but I haven't been able to
find a workaround yet. Sort seems to operate on the resi and ignores the ID
& chain.
Is this a bug or am I doing something wrong?
Thanks,
Spencer
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