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 (depending on the compilers in your computer) >gfortran -static -O3 -ffast-math -lm -o $1 $1.f or >g77 -static -O3 -o -lm $1 $1.f The following is the head of 'spicker.f', which can be helpful for you to prepare your decoy inputs and explain the output results: ******************************************************************************* * SPICKER_3.0, released on Spril 21, 2016 * * This program, Structure-PICKER (SPICKER), aims at selecting the * best fold of lowest free-energy by clustering structural decoys * generated by I-TASSER or other protein structure assembly simulations. * Comments and bug reports should be addressed to zhanglab@zhanggroup.org * * Reference: * Y Zhang, J Skolnick, Journal of Computational Chemistry, 2004 25: 865-871 * * Permission to use, copy, modify, and distribute this program for * any purpose, with or without fee, is hereby granted, provided that * the notices on the head, the reference information, and this * copyright notice appear in all copies or substantial portions of * the Software. It is provided "as is" without express or implied * warranty. ******************* Updating history ************************************ * 2009/01/24: A bug with regard to the input format is fixed * 2010/08/02: SPICKER V2.0 is released. A new option is added to * automatically tune RMSD cutoff based on variation of * decoy distributions. This option works best for decoys * generated by ab initio simulations, such as QUARK. * 2010/09/14: modified 'seq.dat' to a simplied format * 2010/12/29: modified 'rmsinp' to a simplied format * 2016/04/21: added an option to cluster decoys using 1/TM-score to replace * RMSD as the distance scale. This part is written by * Dr. Jens Thomas. ************************************************************************* * * Input files includes: * 'rmsinp'---Mandatory, length of protein & piece for RMSD calculation * 'seq.dat'--Mandatory, sequence file, for output of PDB models * 'tra.in'---Mandatory, list of trajectory names used for clustering * In the first line of 'tra.in', there are 3 parameters: * par1: number of decoy files * par2: 1, default cutoff, best for clustering decoys from * template-based modeling; * -1, cutoff based on variation, best for clustering * decoys from ab initio modeling. * -2, cluster based on 1/TM-scores * par3: 1, select closc from all decoys; * -1, closc from clustered decoys (slighly faster) * From second lines are file names which contain coordinates * of 3D structure decoys. All these files are mandatory. See * attached 'rep1.tra1' etc for the format of decoys. * 'rep1.tra1', 'rep2.tra1', ... ---decoy files which should have the * same name as those listed in 'tra.in'. In the first line, * the first number is the length of the decoy; the second * number is the energy of the decoy (if you donot know the * energy you can put any number there); the third and fourth * numbers are not necessary and useless. * Starting from the second line, the coordinates (x,y,z) of * C-alpha atoms are listed. * 'CA'-------Optional, native structure, for comparison to native. * * Output files includes: * 'str.txt'-----list of structure in cluster; * 'combo*.pdb'--PDB format of cluster centroids; * 'closc*.pdb'--PDB format of structures closest to centroids; * 'rst.dat'-----summary of clustering results; * * Important data and explanations in 'rst.dat': * ------------ summary of clusers ------------------- * i Size R_cut density R_cl_co <E> 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 * --------------------- --------------------- * i N_in <R_in> <Rc_in> N_ex <R_ex> <Rc_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 * * Size------number of decoy structures in the cluster * R_cut-----RMSD cutoff for defining the clusters * density---size/R_cut * R_cl_co---RMSD distance between combo and closc * <E>-------average energy of decoys in the cluster * #str & Trajectory----in this example, the cluster center of the first * cluster comes from 57th decoy in 'rep2.tra1' * N_in------number of structure decoys in the cluster (=size) * <R_in>----average RMSD of decoys to cluster center * <Rc_in>---average RMSD of decoys to cluster centroid * (in I-TASSER, cluster_density=N_in/<Rc_in>) * N_ex------number of structure decoys in the cluster, after excluding * decoys from previous clustering * <R_ex>----average RMSD of decoys to cluster center, after excluding * decoys from previous clustering * <Rc_ex>---average RMSD of decoys to cluster centroid, after excluding * decoys from previous clustering * *******************************************************************************