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

Francesco Pietra chiendarret at gmail.com
Sun Oct 7 01:55:47 PDT 2018

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.
> 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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