git clone -b paper-version https://github.com/DrDongSi/Ca-Backbone-Prediction.git
The program of mapping protein sequences into protein Ca trace drives from cryoEM image data
(1) Download CaTrace2Seq package (short path is recommended)
git clone https://github.com/DrJieHou/CaTrace2Seq.git
cd CaTrace2Seq
(2) Configure CaTrace2Seq (required)
perl setup_env.pl
(3) Run CaTrace2Seq (required)
sh run_CaTrace2Seq.sh <path of fasta sequence> <path of Ca trace> <length threshold for fragment> <output-directory> <num of cpus>
(4) Practice the examples
cd example
sh run_6272.sh
*****************************************************************************
* TM-SCORE *
* A scoring function to assess the quality of protein structure predictions *
* Based on statistics: *
* 0.0 < TM-score < 0.17, Random predictions *
* 0.4 < TM-score < 1.00, Meaningful predictions *
* Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710 *
* For comments, please email to: [email protected] *
*****************************************************************************
Structure1: /home/jh7x Length= 397
Structure2: 6272/pdb3j Length= 397 (by which all scores are normalized)
Number of residues in common= 397
RMSD of the common residues= 2.150
TM-score = 0.9314 (d0= 7.20, TM10= 0.9314)
MaxSub-score= 0.7438 (d0= 3.50)
GDT-TS-score= 0.8086 %(d<1)=0.5819 %(d<2)=0.7431 %(d<4)=0.9093 %(d<8)=1.0000
GDT-HA-score= 0.6039 %(d<0.5)=0.1814 %(d<1)=0.5819 %(d<2)=0.7431 %(d<4)=0.9093
-------- rotation matrix to rotate Chain-1 to Chain-2 ------
i t(i) u(i,1) u(i,2) u(i,3)
1 -0.0638134694 0.9999870448 0.0020705458 0.0046500556
2 0.0280063468 -0.0020814379 0.9999950989 0.0023387491
3 0.1425030895 -0.0046451903 -0.0023483976 0.9999864535