How to install and run spicker? 1, download and unpack spicker.tar.gz. 2, run ./spicker. If the program does not run, you may need to re-compile spicker.f in your computer. The current version is compiled by >pgf77 -Mextend -O -s -fast -Wl,-static -o $1 $1.f If you do not have pgf77, you can also use >g77 -static -O3 -o $1 $1.f -lm The following is the head of spicker.f, which can be helpful for you to prepare your decoy inputs. ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc c c This program, Structure-PICKER (SPICKER), is aimed at selecting the c best fold by clustering trajectors produced by I-TASSER. c For the decoys by other algorithms, the parameters of c (RMSD_cut_initial,RMSD_cut_min,RMSD_cut_max) may need to c be tuned to obtain the best result. c Comments and bug reports should be addressed to yzhang@ku.edu. c c Input files includes: c 'rmsinp'---Mandatory, length of protein & piece for RMSD calculation; c 'seq.dat'--Mandatory, sequence file, for output of PDB models. c 'tra.in'---Mandatory, list of trajectory names used for clustering. c files in 'tra.in'---Mandatory, trajectories of structures. c 'CA'-------Optional, native structure, for comparison to native. c c Output files includes: c 'rst.dat'-----summary of clustering results; c 'str.txt'-----list of all structure in each cluster; c 'RMSD.list'---RMSD to native of all decoys c 'combo*.pdb'--PDB format of cluster centroids; c 'closc*.pdb'--PDB format of structures closest to centroids; c c Reference: c Yang Zhang, Jeffery Skolnick. "SPICKER: Approach to clustering c protein structures for near-native model selection." c Journal of Computational Chemistry, vol 25, 865 (2004). c cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc Important data and explanations: In 'rst.dat': ------------ summary of clusers ------------------- i Size R_cut density R_cl_co E_model #str Trajectory B-------------------------------------------------- 1 109 5.90 18. 1.67 -2200.5 -2272.2 57 rep2.tra1 2 12 5.90 2. 0.70 505.6 580.4 5 rep1.tra1 3 11 5.90 2. 0.97 742.9 926.9 1 rep1.tra1 4 19 5.90 3. 0.66 -2062.5 -2057.1 26 rep1.tra1 5 6 5.90 1. 0.44 219.5 215.0 13 rep1.tra1 6 6 5.90 1. 0.61 -816.8 -801.1 17 rep1.tra1 7 2 5.90 0. 0.40 1694.8 1708.3 2 rep2.tra1 8 2 5.90 0. 0.56 -383.2 -381.6 18 rep2.tra1 9 2 5.90 0. 0.31 -1104.6 -1147.7 22 rep2.tra1 10 1 5.90 0. 0.00 4363.0 4363.0 1 rep2.tra1 --------------------- --------------------- i N_in N_ex C--------------------------------------------- 1 109 3.31 2.75 109 3.31 2.75 2 12 1.54 0.92 12 1.54 0.92 3 11 1.72 1.19 11 1.72 1.19 4 19 1.27 1.15 9 1.10 1.03 5 6 0.96 0.69 6 0.96 0.69 6 6 0.92 0.70 6 0.92 0.70 7 2 0.40 0.40 2 0.40 0.40 8 2 0.56 0.56 2 0.56 0.56 9 2 0.31 0.31 2 0.31 0.31 10 1 0.00 0.00 1 0.00 0.00 R_cut-----RMSD cutoff for defining the clusters R_cl_co---RMSD distance between combo and closc -------average energy of decoys in the cluster #str & Trajectory----in this example, the cluster center of the first cluster is from 57th decoy in 'rep2.tra1' ---cluster density=N_c/