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rcsb / mmtf

The specification of the MMTF format for biological structures
http://mmtf.rcsb.org/
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_struct_conn group missing #4

Open BobHanson opened 8 years ago

BobHanson commented 8 years ago

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 commented 8 years ago

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 commented 8 years ago

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.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/rcsb/mmtf/issues/4#issuecomment-214420328

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 commented 8 years ago

The Chimera team also expressed interest to have those bonds.

arose commented 8 years ago

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.