Hi all, Related to the question I had a few days ago about how chains are displayed in PyMol, some ideas below say it is ok to delete SegIDs that exist in columns 73-76 (and thanks for them).
For anyone who tried deleting SegIDs before, does it affect the pdb file? or is it “safe” to do it? I have another molecule with 4 asymmetric units, and every chain has multiple SegIDs. And of course the segments show each chain is split in PyMol. Thanks very much for any help, Remie On Aug 8, 2014, at 7:32 PM, Marlene Holder <[email protected]> wrote: > 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 16:20, Remie Fawaz-Touma wrote: >> 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 >>>> >>> >>> >> >
