Bug 291210

Summary:	sci-libs/monomer-db needs attached patch
Product:	Gentoo Linux	Reporter:	Justin Lecher (RETIRED) <jlec>
Component:	Current packages	Assignee:	Justin Lecher (RETIRED) <jlec>
Status:	RESOLVED LATER
Severity:	normal	CC:	sci-chemistry
Priority:	High
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---
Attachments:	standard-residue-torsions.patch

Description Justin Lecher (RETIRED) gentoo-dev

2009-10-30 18:43:24 UTC

Quoting Paul Emsley from ccp4-dev ml:


It seems to me that the dictionary for several standard residues need
to be updated [1].

My reading of the IUB-IUPAC convention is that the primary torsion is
relative to the xx1 atom (not the xx2 atom).  This caused me confusion
for a while when I was using the dictionary to set the torsions of
roamers by using the dictionary definitions of the torsions.

Relatedly, it seems to me that to reduce the occurrence of
nomenclature errors in VALs and LEUs, the chiral centre sign should be
changed from the (too liberal) "both" to "negativ".

The combination of the incorrect atom for setting torsions in LEUs,
combined with the nomenclature errors in the model have lead to many
"decoy leucines" [2].  Let's clean things up.

The patch is attached.

Paul.

[1] following conversations with Jeff Headd and Gert Vriend, I should add
[2] See for example residue 105 from 1A0J.

Comment 1 Justin Lecher (RETIRED) gentoo-dev

2009-10-30 18:44:21 UTC

Created attachment 208760 [details]
standard-residue-torsions.patch

standard-residue-torsions.patch

Comment 2 Justin Lecher (RETIRED) gentoo-dev

2009-11-02 19:43:19 UTC

Decided with dberkholz to stick to Garibs (sci-chemistry/refmac) nomenclature.