[Chimera-users] SEQRES not read properly?

Eric Pettersen pett at cgl.ucsf.edu
Wed Jul 24 13:15:00 PDT 2019

Is there some reason you’re trying to put several distinct chains into the same chain A?  Unfortunately, Chimera is too “smart” for this.  It looks at both of the residues you’ve numbered 1218 (with a TER card in between) and sees they are too far apart physically to be consecutive in sequence and inserts a sequence gap between them rather than the start of the chain.  I don’t think there is anything you can do about this other than assign distinct chain IDs to the sequences that are in fact different physical chains.  Well, if there are in fact missing residues there, you could update the SEQRES records to reflect that, then things would probably work.  You should also renumber things to avoid having residues with the same sequence number and chain ID.


> On Jul 24, 2019, at 5:04 AM, Danilo Boškovic <a01406823 at unet.univie.ac.at> wrote:
> Dear all,
> I combined a PDB file from three chains to single chain format. In between those chains are TER. Now i need to add missing residues as SEQRES. I added them all properly, all atoms are named properly but chimera detects a missing residue at last position instead of the first position of chain B making the whole sequence shift for 1 nucleic acid residue to the left. Pymol, which does not read SEQRES, registers all missing residues as blanks and their positions are 100% correct (checked 3 times). SEQRES was copied from the three-chain PDB file and edited to resemble a single chain file (C and E were renamed to A, SEQRES numbering was continued uninterrupted). How does chimera read SEQRES? Here is the full pdb file in gist:
> https://gist.github.com/danilob2929/34c303a5b1981f0a60942bc322052672
> Thanks in forwards,
> D.B.
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