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.
There is just one thing that I might think could be causing the problem: in PyMol, when I display the sequence, I see: /B/ for the ligand, /C/ for waters and /A//A/ for the protein, why are there two As? I could not explain that from the text pdb file Is having two As related to the fact that chain A does not appear first? How can I fix this? Thank you very much for any idea, Remie On Aug 8, 2014, at 8:50 AM, Avinash Punekar <[email protected]> wrote: > 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 resSeq (i.e. all the > atoms of the first residue in chain A should be numbered 1 and so on). There > are several programs that can do this, pdbset in CCP4 suite, pdbeditor > (http://www.bioinformatics.org/pdbeditor/wiki/) or even online > (http://www.canoz.com/sdh/renumberpdbchain.pl). > > Best regards, > Avinash On Aug 7, 2014, at 3:22 PM, Philip Kiser <[email protected]> wrote: > Hi Remie, > > How about copying each component into a separate text file (with the unit > cell, scale records, etc included in each) and then loading them into Pymol > in the desired order. I know this isn't very elegant, but it might work okay > if you only have to do it a few times. > > Good luck, > Philip > > > On Thu, Aug 7, 2014 at 3:17 PM, Remie Fawaz-Touma <[email protected]> > wrote: > 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 to the ligands and put them right after the ligand > atoms list (even though I didn’t think it matters), but I still have the same > problem: PyMol shows chain B first in the sequence display. > > Any suggestion? > > Thank you, > Remie > > > On Aug 7, 2014, at 2:30 PM, Tim Gruene <[email protected]> wrote: > >> 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 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 chains in coot: Extensions > >>> Modelling > Reorder chains, and chain A is my protein, B is the ligand and >>> C are the waters. >>> >>> So why don?t I see the same order in PyMol and how do I fix that? >>> >>> Thanks for any help, >>> >>> Remie >> >> -- >> -- >> Dr Tim Gruene >> Institut fuer anorganische Chemie >> Tammannstr. 4 >> D-37077 Goettingen >> >> GPG Key ID = A46BEE1A >> > >
