Dear Remie,
the first A is the segment identifier and the second A is the chain
identifier. You might have missed it but there was an email today from
Thomas Holder solving exactly this problem. See below:
On 07.08.2014 19:40, Thomas Holder wrote:
Hi Remie,
PyMOL by default sorts atoms based on their identifiers (segment, chain,
residue number). Could it be that your file has segment identifiers? Try this
after loading your file:
PyMOL>alter all, segi=""
PyMOL>sort
Cheers,
Thomas
Read about the PyMOL slash notation here:
http://www.pymolwiki.org/index.php/Selection_Macros
Cheers,
Marlene
On 08.08.2014 18:32, Avinash Punekar wrote:
Dear Remie,
May be you have saved the coordinates as A.pdb? In that case the first /A/ will
be the file name followed by the second /A/ for the protein chain. Else,
somewhere in the pdb you may have an empty atom record, which is very unlikely.
Best regards,
Avinash
