0000034: Packer won't mutate a post-trans-mod residue

Notes
(0000082) smlewis (Administrator) 2012-08-22 16:24	not assigned: returning to red angry

(0000294) smlewis (Administrator) 2013-05-13 11:31	Some notes from the email thread about this: the problem here is in variant matching. In this function: void ResidueLevelTask_::allow_noncanonical_aa( ... if ( original_residue_type_->variants_match( *aas_iter ) && There is a variant matching check. If you start sulfated, ONLY sulfated variants match and will be allowed. EMPTY does not affect original_residue_type_ and will have no effect here. This is perfectly strict variant matching. You require weaker matching, which ignores mismatches due to some* variants (sulfated, etc) and prevents mismatches due to other variants (chainbreak, terminus, etc). You can try tweaking this check to not care about your subset of variants: perhaps a flag "allow_design_tofrom_PTMs", and then modify this check to ignore variant mismatches caused by some curated set of variants (sulfated, phosphorylated, etc). You can try removing this check. It will have nasty side effects like Rosetta will try packing the chainbreak variants or terminus variants into the middle of the chain. Hopefully the scorefunction will reject that. Moving TYR plus S to its own params file as TYS may work. Doug corrects me on the Dunbrack lookup (good). After further thought, I also realize that Rosetta ignores the PDB standard, in that it names sulfated tyrosine TYR and adds a sulfate if those atoms are present, but the PDB uses TYS. So, creating a S-TYR residue type file, with the name and name3 TYS, would fix your variant matching problem AND improve the PDB reader to be more standard-compliant. This may cause the reverse problem, however, where TYR becomes able to mutate to TYS in all cases. The ResidueLevelTask constructor uses variant matching just like the troublesome allow_noncanonical_aa function, and it will let all aa_tyr pass equally (this is how HIS and HIS_D both work.). Currently the code distinguishes via "is_protein" and the aa type being aa_unk - perhaps there is need for a third level of distinction for chemically modified but not aa_unk residues - they should be treated with the aa_unk logic.

Issue History
Date Modified	Username	Field	Change
2012-07-02 15:19	smlewis	New Issue
2012-07-02 15:19	smlewis	Status	new => assigned
2012-07-02 15:19	smlewis	Assigned To	=> smlewis
2012-07-31 16:07	smlewis	Assigned To	smlewis =>
2012-08-22 16:24	smlewis	Note Added: 0000082
2012-08-22 16:24	smlewis	Assigned To	=> smlewis
2012-08-22 16:24	smlewis	Status	assigned => new
2012-08-29 08:34	smlewis	Assigned To	smlewis =>
2012-09-04 19:32	Labonte	Tag Attached: design
2012-09-04 19:32	Labonte	Tag Attached: PackerTask
2012-09-04 19:32	Labonte	Tag Attached: packing
2012-09-04 19:32	Labonte	Tag Attached: resfile
2013-05-13 11:28	smlewis	Assigned To	=> jwillis0720
2013-05-13 11:28	smlewis	Status	new => assigned
2013-05-13 11:31	smlewis	Note Added: 0000294

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