There are atom records for C, O and CA (B-factors 42, 43, 40A**2,
respectively), but not for N, as density tapers off going to the amino
terminus (well, without the "amino" in this case). Residue 3 is the
lowest-numbered residue in its chain. B-factors of N, CA of residue 4 are
38, 33A**2, respectively. Could refmac just be taking exception to the
missing N atom?
---------- Forwarded message ----------
From: Ethan Merritt <merr...@u.washington.edu>
Date: Tue, Jul 24, 2012 at 11:27 AM
Subject: Re: [ccp4bb] Refmac: ADP is non-positive
To: wtempel <wtem...@gmail.com>
Cc: CCP4BB@jiscmail.ac.uk
On Tuesday, 24 July 2012, wtempel wrote:
> CCP4ers,
>
> a log file from Refmac_5.7.0027 presents me with this line:
>
> <fromLog>
> Problem with the ADP of the atom N A 3 ADP is non-positive
> -1.7740907E+35
> </fromLog>
>
> I did not explicitely refine ADPs or TLS.
> Should I modify my model when I encounter such a message? If yes, does the
> message refer to a specific atom, such as atom N of residue 3 in chain A?
I
> should note that that atom is omitted from my model due to lack of
electron
> density/disorder.
What do you mean by "omitted from the model"?
Are there no ATOM records for that residue in the PDB file?
What are the B factors for the other atoms in that region?
Ethan
>
> Many thanks in advance,
> Wolfram Tempel
>
