Thank you so much Thomas and Marlene, yea I missed the email from Thomas the
first time.
Your suggestion solved my problem. I appreciate your help very much,
Remie
On Aug 8, 2014, at 7:35 PM, Marlene Holder
wrote:
> Dear Remie,
>
> the first A is the segment identifier and the second A is th
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 base
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
Thanks for all the valuable comments.
In fact, chain “A” shows up first in my pdb, then comes “B” then “C”.
Also the atom/hetatm number are in order starting from the first atom all the
way to the end.
And resSeq number is in order, protein (which is chain A) 9-694, then ligand
starts at 836.
Dear Remie,
PyMol considers both chain identifier (chainID, column 22 in a PDB file) as
well as the Residue sequence number (resSeq, columns 23-26 in a PDB file) to
show the order of arrangement. So, simply renaming chainID’s will not work. In
addition to that you will also have to renumber the
Hi Dr. Gruene,
Thanks for your input.
I have actually checked pdb and the chains are listed in the order A, B then C;
except for the LinkR between the ligand units and between some amino acids
where there are gaps (those link records were towards the top), so I moved
those LinkR corresponding
Dear Remie,
did you check (with a text editor) the PDB file saved from coot if it actually
reordered the chains inside the file? Maybe chain C is still listed first, and
maybe this is what pymol takes as order.
Regards,
Tim
On Thu, Aug 07, 2014 at 11:19:42AM -0400, Remie Fawaz-Touma wrote:
> Hi
Hi everyone,
Does anyone know how to rearrange chains when looking at a structure in PyMol
(maybe it has to be done in coot, don’t know).
I have the ligand first now in PyMol and would like to see the sequence of the
protein first, then ligand.
It is worth mentioning that I did reorder the ch
