[Chimera-users] Fwd: error opening .cif file
meng at cgl.ucsf.edu
Sun Oct 7 10:50:16 PDT 2018
I believe Chimera is using the auth_seq_id (author residue numbering). In mmCIF, there is also another residue numbering value, label_seq_id, and sometimes they are different. Usually there is some reason why the authors numbered differently, but I don’t know in this case.
If it bothers you, you can just renumber the chain sequentially (Tools.. Structure Editing… Renumber Residues, or command “resrenumber”).
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On Oct 7, 2018, at 1:55 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
> Hi Elaine:
> If the deposited sequence for 4i4t is correct, the deposited pdb is wrong (void between 42-45 and 360-369 in chain D).
> The deposited cif file is correct, however, for reasons that I do not know, chimera follows the error that I said above in extracting pdb. VMD extracts correctly the pdb, at least as far as chain D is concerned (no voids, so that 431 residues, as indicated on RCSB, i.e., missing 442-455).
> Best regards
> ---------- Forwarded message ---------
> From: Francesco Pietra <chiendarret at gmail.com>
> Date: Sat, Oct 6, 2018 at 9:43 PM
> Subject: Re: [Chimera-users] error opening .cif file
> To: chimera <chimera-users at cgl.ucsf.edu>
> Hi Elaine
> I had better waited, examining the sequence, before claiming an error.
> I'll also update chimera.
> On Sat, Oct 6, 2018, 19:10 Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Francesco,
> The PDB and mmCIF files for 4i4t have chain D 42 directly bonded to 45, and no residues 43 or 44. Although I have no idea why the data is like this, I believe Chimera is reading the file correctly.
> Your version of Chimera is a couple of years old (1.11 is from 2016 and 1.13 was released this year), but that would not have any effect on this issue.
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Oct 6, 2018, at 8:39 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
> > Hi
> > With my /opt/UCSF/Chimera64-1.11.2/bin/chimera, I notice a mistake in opening 4i4t.cif.gz (as 4i4t.cif), i.e., residue 43 and 44 in chain D are mis-numbered 44 and 45, giving the wrong impression that residues 43 and 44 are missing. I have not checked anything else.
> > cheers
> > francesco pietra
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