RosettaRemodel can not work now?

[Anonymous]

Hi, everybody, the RosettaRemodel in Rosetta3.4 and Rosetta3.5 seems not to work.

There is no executable file like “remodel.macosgccrelease” and no example in the “rosetta/rosetta_tests/tests/remodel/”, why? thank you.

[Anonymous]

Hi,

From what I have been told, it was included in the first weekly release. Try that, and let us know if you run into any problems.

[Anonymous]

Hi, jadolfbr

There is something wrong as follows:

The constraint file:
CST::BEGIN
TEMPLATE:: ATOM_MAP: 1 atom_name: SG CB CA
TEMPLATE:: ATOM_MAP: 1 residue1: C

TEMPLATE:: ATOM_MAP: 2 atom_type: Nhis,
TEMPLATE:: ATOM_MAP: 2 residue1: H

CONSTRAINT:: distanceAB: 3.00 1.80 1.0 1

CST::END

Blueprintfile:
1 T .
2 E .
…..

106 V .
107 C . CST1A
108 T .
…..
150 V .
151 P .
152 P .
153 S .
154 K .
155 E E
156 I E
157 K E
158 V E PIKAA H CST1B
159 W E
160 D .
……

The command:
../../source/bin/remodel.linuxgccrelease -database ../../database/ -s 1UGQ-renumber.pdb -remodel:blueprint Blueprint.1UGQ -run:chain A -enzdes:cstfile C-cst.enzdes.cst -remodel:num_trajectory 2 -overwrite -remodel:quick_and_dirty -run:constant_seed

Error:
core.chemical.ResidueType: atom name : CEN not available in residue HIS
core.chemical.ResidueType: N
core.chemical.ResidueType: CA
core.chemical.ResidueType: C
core.chemical.ResidueType: O
core.chemical.ResidueType: CB
core.chemical.ResidueType: CG
core.chemical.ResidueType: ND1
core.chemical.ResidueType: CD2
core.chemical.ResidueType: CE1
core.chemical.ResidueType: NE2
core.chemical.ResidueType: H
core.chemical.ResidueType: HD1
core.chemical.ResidueType: HA
core.chemical.ResidueType: 1HB
core.chemical.ResidueType: 2HB
core.chemical.ResidueType: HE1
core.chemical.ResidueType: HD2
core.chemical.ResidueType:

ERROR: unknown atom_name: HIS CEN
ERROR:: Exit from: src/core/chemical/ResidueType.cc line: 2027
protocols.jd2.JobDistributor:

[ERROR] Exception caught by JobDistributor for job 1UGQ-renumber_0001

[ERROR] EXCN_utility_exit has been thrown from: src/core/chemical/ResidueType.cc line: 2027
ERROR: unknown atom_name: HIS CEN

protocols.jd2.JobDistributor: 1UGQ-renumber_0001 reported failure and will NOT retry

Could you give me a hand? thanks!

[Anonymous]

I get the answer, we need change the 158V to 158H first,then apply the constraint, it is OK.

[Anonymous]

Hi, everybody

I find an interesting thing!

It seems that the “remodel part” of protein always changes to “V” whatever the secondary structure is set.

Did anyone have the experience? Thanks.

[Anonymous]

Thanks to rmoretti.

It seems that the “remodel part” of protein always changes to “V” whatever the secondary structure is set.

like the picture in the attachment. why?

the sequence VVVRVVV is remodeled.

[Anonymous]

If you’re pre-mutating your input structure to H, make sure you update your blueprint file to match. Otherwise the remodel part might get confused regarding if it’s working with a H or V residue.

[Anonymous]

Oh, yeah. Valine is used in many centroid situations as an “average” amino acid. When you’re doing backbone remodeling, you need to have some idea of the size of the sidechain, even if you’re going to allow design at that location later. Valine is a good stand in amino acid in those contexts.

My guess is that when the remodel code sees that you’re going to be remodeling the (especially if you’re going to change it with redesign) it will change the identity to V for the remodeling process. The intermediate structures (e.g. just out of centroid) might then have valine at those positions. Once you go through the full atom design stages, however, the desired amino acid identities should be imposed at those positions, and the valines should disappear, except for those locations where they are allowed.

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