0000151: disulfide energy terms do not handle D-cysteine

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0000151

Rosetta

[All Projects] Incorrect Results

public

2012-11-08 09:31

2017-08-07 19:56

Reporter

smlewis

Assigned To

amw579

Priority

low

Severity

minor

Reproducibility

unable to reproduce

Status

closed

Resolution

fixed

Platform

All platforms

Any

OS Version

Any

Product Version

All

Fixed in Version

Summary

0000151: disulfide energy terms do not handle D-cysteine

Description

The D-cysteine parameters file DCYD.params is set up like CYD.params for disulfide bonding. However, the disulfide energy term explicitly checks for "aa_cys" in the aa enum; DCYD is aa_unk (because it uses a different set of rotamers, I believe).

These bits of code are certainly at fault:
rosetta_source/src/core/scoring/disulfides> ack-grep aa_cys
DisulfideMatchingEnergyContainer.cc
560: if ( res.aa() == chemical::aa_cys &&
622: if ( res.aa() != chemical::aa_cys ||
632: } else if ( pose.residue( ii ).aa() == chemical::aa_cys &&

CentroidDisulfideEnergyContainer.cc
566: if ( res.aa() == chemical::aa_cys &&
618: if ( res.aa() != chemical::aa_cys ||
628: } else if ( pose.residue( ii ).aa() == chemical::aa_cys &&

FullatomDisulfideEnergy.cc
184: return res_moving_wrt_eachother && res1.aa() == aa_cys && res2.aa() == aa_cys &&
440: if ( rsd1.aa() != chemical::aa_cys || rsd2.aa() != chemical::aa_cys ) return;

FullatomDisulfideEnergyContainer.cc
566: if ( pose.residue( ii ).aa() == chemical::aa_cys &&
615: if ( pose.residue( ii ).aa() != chemical::aa_cys ||
625: } else if ( pose.residue( ii ).aa() == chemical::aa_cys &&

DisulfideMatchingEnergy.cc
124: if ( rsd1.aa() != chemical::aa_cys || rsd2.aa() != chemical::aa_cys ) return;

CentroidDisulfideEnergy.cc
130: if ( rsd1.aa() != chemical::aa_cys || rsd2.aa() != chemical::aa_cys ) return;

There may be other relevant code in the disulfide-creation machinery.

Line numbers are SVN 52071.

Additional Information

It is not clear to me that DCYD should be energetically equivalent to L-disulfides. Certainly the SG-SG term dslf_ss_dst is the same. The angle dslf_cs_ang is probably the same. I don't know about the dihedrals, but from the commentary in FullatomDisulfidePotential.cc it seems the potentials are roughly symmetric, implying that they are not "perfect" for D-disulfides but better than just refusing to handle D-disulfides.

Issue History
Date Modified	Username	Field	Change
2012-11-08 09:31	smlewis	New Issue
2017-08-07 19:56	amw579	Fixed in SVN Version	=> n/a
2017-08-07 19:56	amw579	Status	new => closed
2017-08-07 19:56	amw579	Assigned To	=> amw579
2017-08-07 19:56	amw579	Resolution	open => fixed

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