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create a centroid file from structure or NOE list

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create a centroid file from structure or NOE list

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

Post Situation: 
Wed, 2013-03-20 12:23

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.)

Wed, 2013-03-20 17:57

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.


Thu, 2013-03-21 07:30

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.

Thu, 2013-03-21 08:16