Maybe
sort_chains(imol)
is what you want.
Additionally or alternatively, change the order or the SSBOND or LINK
header records.
HTH.
Paul.
On 07/12/2020 18:59, Christian GALICIA wrote:
Dear Folmer,
Thank you for your answer. Only one out several chains is bound to a
ligand in the structure, the aim is to convert the ligand-bound chain
into chain A after suggestion of a reviewer. When I open the pdb file
on a text editor I expect this chain to be listed before the other
chains, which doesn't happen. Also, I when I display the sequence of
the protein in pymol I expect to see chain A at the beginning, which
doesn't happen once the file is converted to cif.
Best,
Christian
------------------------------------------------------------------------
*From:* Folmer Fredslund <folm...@gmail.com>
*Subject:* [ccp4bb] how to swap chain IDs
*Date:* Monday, December 7, 2020, 19:44
*To:* Christian GALICIA
*Cc:* CCP4BB@jiscmail.ac.uk
Dear Christian
What exactly are you trying to accomplish?
I don't quite follow why you would expect the atom positions to change?
Unless I'm missing something?
Also, why would you expect the numbering to change when you edit the
chain ID?
After CIF conversion:
What do you mean by "original position"? What position where you
expecting?
And you mention that chain A is not at the beginning of the sequence.
What sequence are you talking about?
Coot or pdbset can definitely do want you want, I'm just not sure
what exactly you're after.
Perhaps a more elaborate explanation would be good?
Best regards
Folmer Fredslund
man. 7. dec. 2020 18.49 skrev Christian GALICIA
<christian.galicia.diaz.sant...@vub.be
<mailto:christian.galicia.diaz.sant...@vub.be>>:
Hello,
I'm trying to swap the chain IDs of a structure. I tried changing
the IDs in coot and with PDBset, both change labels of the chains
but not the atom positions nor numbering.Also, after the pdb file
is converted to cif for deposition it displays in pymol in the
original position making chain A not to be at the beginning of
the sequence. I would appreciate if you would suggest a good way
to achieve this. The structure is otherwise finished and will no
go any other rounds of refinement. Thanks
Christian
--
*Christian Galicia*
E-mail: cgali...@vub.be <mailto:cgali...@vub.be>
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