[Chimera-users] Fwd: error opening .cif file

[Elaine Meng]

Hi Francesco,
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”).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/renumber.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/resrenumber.html>

Best,
Elaine
-----
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
> francesco
> 
> ---------- 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.
> francesco
> 
> 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.
> Best,
> Elaine
> -----
> 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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