create a centroid file from structure or NOE list

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    • #1535

        I’m using an ab initio script to preform a structure calculation with NOE restraints (i,i+3 or longer). The _fa NOE file, as I understand it, only activates at one stage. Is it better to create a centroid file for earlier stages of the calculation? Is it necessary ?

        As well, would someone be willing to share a structure generation script with me ? I’m sure I could be doing it better. As things go, I have method to generate a little protein structure from NOEs and coordinate a Zn ion with 3xCys/1xHis, below. I would appreciate the help to make it better and more efficient.

        thank you (again, since I just posted a cst question)

        -nstruct 1
        -database /Applications/Darwin/rosetta3.4/rosetta_database
        -in:file:fasta input/pp10.trim.fasta
        -in:file:frag3 input/pp10.trim.frags3.dat.gz
        -in:file:frag9 input/pp10.trim.frags9.dat.gz
        -jumps:residue_pair_jump_file input/pp10.zn.jump
        -constraints:cst_file input/pp10.zn.cen.cst
        -constraints:cst_fa_file input/pp10.fa.cst
        -constraints:cst_weight 1
        -constraints:cst_fa_weight 1

        -abinitio::increase_cycles 10
        -abinitio::rg_reweight 0.5
        -abinitio::rsd_wt_helix 0.5
        -abinitio::rsd_wt_loop 0.5
        -score::weights score12_full
        -out:file:scorefile decoys/
        -out:file:silent decoys/default.out

      • #8512

          Constraints: it is definitely better to use centroid constraints than fullatom constraints. (Using both is fine.) Centroid mode is made for allowing large conformational sampling; fullatom mode only samples within whatever potential well centroid mode found. Therefore, the constraints will work much better in centroid mode. Just be careful to only constrain on centroid-present atoms (which includes the amide hydrogen and all backbone heavyatoms, but usually not HA).

          (I don’t have a script for this other than the resources we discussed – hopefully someone else will.)

        • #8515

            There is a are two scripts in the CS_ROSETTA distribution, and The CB script outputs HA atoms but I think the CB/CEN atom mapping table can be modified to account for that.

            My molecule folded well when I included some centroid restraints. Oliver Lange has graciously offered his help to suggest improvements to my method.


          • #8519

              There is a patch file that adds HA atoms to centroids, I’m just not sure how it’s activated – if you have need for HA we can look it up.

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