RosettaRemodel can not work now?

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    • August 13, 2013 at 11:56 pm #1693
      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.

      • August 14, 2013 at 3:07 pm #9204
        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.

        • August 19, 2013 at 12:33 am #9210
          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!

          • August 19, 2013 at 7:21 am #9212
            Anonymous

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

            • August 27, 2013 at 6:39 am #9241
              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.

              • September 3, 2013 at 12:16 am #9274
                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.

                • August 29, 2013 at 6:09 pm #9245
                  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.

                  • September 3, 2013 at 6:51 pm #9278
                    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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