_struct_conn group missing

[BobHanson]

Just notice that although we have all the bonding between amino acids and all the bonding within groups, we are missing the very important ones in _struct_conn, particularly in 1BLU

I believe this may be because the "metalc" type is being skipped. This is an important type to include.

metalc1 metalc ? B SF4 . FE1 ? ? ? 1_555 A CYS 53 SG ? ? A SF4 101 A CYS 53 1_555 ? ? ? ? ? ? ? 2.189 ?

same for 1hho:

metalc1 metalc ? A HIS 87 NE2 ? ? ? 1_555 D HEM . FE ? ? A HIS 87 A HEM 143 1_555 ? ? ? ? ? ? ? 1.937 ?

It is critical that we have these.

[arose]

We currently rely on mmcif files and the chemical component dictionary to get bond information. We felt that the metal bond given in the archive are currently not good enough, so we did not include them.

[BobHanson]

do please include them. Let the user decide if they want them or not.

On Mon, Apr 25, 2016 at 11:06 AM, Alexander Rose notifications@github.com
wrote:

We currently rely on mmcif files and the chemical component dictionary to
get bond information. We felt that the metal bond given in the archive are
currently not good enough, so we did not include them.

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Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

[arose]

The Chimera team also expressed interest to have those bonds.

[arose]

The question boils down to whether we absolutely stick to clean and consistent data for whole-archive analyses or allow some data (like "metal bonds") that is only good for a number of structures and then filter it out at the API level.