I am a new user to the I-TASSER program to predict the 3D structures of protein, and I have downloaded and installed the I-TASSER standalone package(version 3.0) as required in the README.txt. However, when I run this program to predict the 3D structure of an amino acid sequence for test following the requirement in the README.txt strictly, I am confused to find out that my local results are very different with the results by the web server with the same sequence, and the specific situation is that the two cscore files are so similar while the model files corresponding are very distinguishing when aligned and shown by the PyMOL application. I check the my process for a long time and many times, but I still have no idea about what's the problem and how to solve it. I need your help, please! Thanks a lot!
supplementary imformation:
(1)command for running I-TASSER3.0
nohup ./runI-TASSER.pl -pkgdir /data1/yplu/I-TASSER3.0 -libdir /data1/yplu/ITLIB/ -seqname seq.fasta -datadir /data1/yplu/data/9wf43/ -usrname yplu -java_home /usr/local/inspur/share/jdk1.6.0_10/ -runstyle parallel &
(2)my local results and the results by web server
please see attachment