To apply distance constraint to MULTIPLE residue pairs, what’s the format?

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    • April 6, 2009 at 5:24 pm #526
      Anonymous

        Dear All,

        I have a question about distance constraint.

        For single pair of two residues, the following format:

        7.0
        370 A
        371 B

        works. But I need to apply distance constraint to MULTIPLE residue pairs. What is the format? I tried different ways as follows:

        7.0
        1 A
        2 B
        (with or without blank line)
        7.0
        3 A
        4 B

        or:

        7.0
        1 A
        2 B
        3 A
        4 B

        but none of them works.

        Please help. Thank you in advance.

        Shirley

      • April 6, 2009 at 5:25 pm #4061
        Anonymous

          > Dear All,
          >
          > I have a question about distance constraint.
          >
          > For single pair of two residues, the following format:
          >
          > 7.0
          > 370 A
          > 371 B
          >
          > works. But I need to apply distance constraint to MULTIPLE residue pairs. What is the format? I tried different ways as follows:
          >
          > 7.0
          > 1 A
          > 2 B
          > (with or without blank line)
          > 7.0
          > 3 A
          > 4 B
          >
          >
          > or:
          >
          > 7.0
          > 1 A
          > 2 B
          > 3 A
          > 4 B
          >
          > but none of them works.
          >
          > Please help. Thank you in advance.
          >
          > Shirley
          >
          >
          >
          >
          >
          >
          >

        • April 8, 2009 at 4:23 pm #4062
          bpierce
          Participant

            Hi Shirley,

            For rosetta++ the format for constraints (in a .cst file) is like this:

            CB-CB csts from ksync alignment
            measured in 1XZY.pdb
            551
            4 CB 19 CB 18.02 14.02 0.00
            4 CB 20 CB 12.95 8.95 0.00
            4 CB 22 CB 7.62 3.62 0.00
            4 CB 23 CB 9.48 5.48 0.00
            4 CB 24 CB 7.48 3.48 0.00
            …

            The number 551 refers to the total number of constraints in teh file.

            I guess you are using docking. I think docking will also read the above style constraint file (but I’m not 100% sure). Try it and see.

            Vanita.

          • April 9, 2009 at 4:42 am #4064
            Anonymous

              Hi all,

              I have the exact same question as Shirley. Much thanks to Vanita for the reply. However her example gives NOE distance constraints, if I’m not mistaken… Rather than atom-atom distances, I’d like to specify residue-residue distances as requested by Shirley.
              However, Rosetta only reads in the 1st constraint specified… Is there any way to overcome this? Thanks much in advance.

              Regards,
              Shamima

            • April 9, 2009 at 5:22 pm #4066
              Anonymous

                Thank Vanita and Shamima’s response very much. Yes, I would like to specify residue-residue distance, and I intended to use a .dst file and so hope rosetta could accept more than one distance constraints in the .dst file.

                I did try Vanita’s idea while using a .cst file in slightly different format as follows:

                2
                -1000
                1 A
                2 A
                3 A
                4 A
                1 B
                2 B
                3 B
                0 B
                -100
                8 A
                0 A
                filter -10

                It seems to be running, while I’m not sure yet if it’s doing the right thing.

                Any input will be appreciated,

                Shirley

                > Hi Shirley,
                >
                > For rosetta++ the format for constraints (in a .cst file) is like this:
                >
                > CB-CB csts from ksync alignment
                > measured in 1XZY.pdb
                > 551
                > 4 CB 19 CB 18.02 14.02 0.00
                > 4 CB 20 CB 12.95 8.95 0.00
                > 4 CB 22 CB 7.62 3.62 0.00
                > 4 CB 23 CB 9.48 5.48 0.00
                > 4 CB 24 CB 7.48 3.48 0.00
                > …
                >
                > The number 551 refers to the total number of constraints in teh file.
                >
                > I guess you are using docking. I think docking will also read the above style constraint file (but I’m not 100% sure). Try it and see.
                >
                > Vanita.

              • April 10, 2009 at 9:51 am #4067
                Anonymous

                  Hi Shirley,

                  If I’m not wrong, the constraints specified in a .cst file “force” Rosetta to only output decoys that contain those specified residues (1-4, 8 of Chain A and 1-3 of Chain B in your case) at the binding interface. Any decoys that do not include these residues as part of the binding interface are automatically rejected.

                  However, if I’m not mistaken it’s just a “loose definition” of ensuring the residues are present at the binding interface. Which is why I’m trying to achieve a closer (or accurate?) binding by specifying distance constraints in the .dst file, but to no avail thus far as far as multiple residues are concerned.

                  Regards,
                  Shamima

                • April 16, 2009 at 7:36 pm #4069
                  Anonymous

                    Hi Shamima,

                    Thank you for your comments. You are right, the .cst file only poses a loose definition for binding interface residues. I would also like to apply distance constraints in .dst file instead if it were available.

                    Best regards,

                    Shirley

                    > Hi Shirley,
                    >
                    > If I’m not wrong, the constraints specified in a .cst file “force” Rosetta to only output decoys that contain those specified residues (1-4, 8 of Chain A and 1-3 of Chain B in your case) at the binding interface. Any decoys that do not include these residues as part of the binding interface are automatically rejected.
                    >
                    > However, if I’m not mistaken it’s just a “loose definition” of ensuring the residues are present at the binding interface. Which is why I’m trying to achieve a closer (or accurate?) binding by specifying distance constraints in the .dst file, but to no avail thus far as far as multiple residues are concerned.
                    >
                    > Regards,
                    > Shamima

                    • April 21, 2009 at 3:05 pm #4070
                      fabio
                      Participant

                        Unfortunately the .dst format only allows a single restraint between residues pairs in Rosetta++.

                        the docking_read_dist_constraint function in docking_constraint.cc defines how the dst file is read.

                        To add more constraints you would need change the size of the dist_constraint_residue array in interface.cc and also change the evaluation of the constraints in docking_dist_constr_bonus in docking_constraints.cc such that it iterated over all of the multiple constraints that you supply.

                        There are probably a couple of other things that you would need to do as well.

                        Alternatively you may want to ask whether the Rosetta-3.0 docking program can handle multiple residue pairs constraints. It has several advantages built in. Reisdue pair constraints may be one of them.

                        Kristian

                    • June 18, 2009 at 8:13 am #4102
                      nobuyasu
                      Participant

                        hi,
                        But the following contraint is just a docking site constraints.
                        2
                        -1000
                        1 A
                        2 A
                        3 A
                        4 A
                        1 B
                        2 B
                        3 B
                        0 B
                        -100
                        8 A
                        0 A

                        filter -10

                        not distance contraint

                        /// distance constraint file format: (filter only)
                        ///
                        /// 10.0 distance (Angstroms)
                        /// 23 H residue 1
                        /// 24 H residue 2

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