I tracked this error down to mmdb library, and it has nothing to do with
ANISOU records per se (it is indeed highly unlikely that anyone would
implement a rigorous check of matching Uij's to Bs).
Apparently, mmdb expects the element field (77-78 in both ATOM/ANISOU
records) to be filled. My expectation was that if the field is empty it
will be ignored or constructed from the atom name, but apparently it's
not so.
This is obviously not related to coot and in most scenarios the problem
can be alleviated by, say, passing a file through pdbset... Take that
back, pdbset fails too as it apparently is using mmdb. Well, maybe 0
cycles of refmac will produce a readable file. Or maybe there is some
other pdb-fixing tool.
It also appears that mmdb will by default pay attention to the segment
ID, which it reads in positions 71-74 or such. This is not defined in
official PDB format, but mercifully mmdb will only fail if you have a
mismatch - empty segid will be ignored.
Cheers,
Ed.
On Mon, 2011-10-24 at 15:27 -0400, Ed Pozharski wrote:
> I get an error when trying to load a file that contains ANISOU records.
>
> ...
> ERROR 14 READ: Unmatch in different records for the same atom.
> LINE #2
> ANISOU 1 N ASN A 60 8621 383 2100 134 -2339
> 351
> ...
>
> I suspect that it fails because the Uij's from the ANISOU record do not
> match the B-factor listed on the ATOM line, e.g.
>
> ATOM 1 N ASN A 60 23.118 41.711 36.893 1.00
> 93.11
> ANISOU 1 N ASN A 60 8621 383 2100 134 -2339
> 351
>
> The question is, why should it fail in this situation? The only way I
> see the ANISOU records are used is to show the thermal ellipsoids, and
> the mismatches may occur in some other benign situations (e.g. someone
> resetting the B-values manually).
>
> Or is it a bug?
>
> In a particular application I am dealing with the mismatch is deliberate
> and the ANISOU records are used exclusively for visualization purposes.
> This worked in the past.
>
> Ed.
>
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /
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