Consurf server install

0. copy file and mkdir bin

1. tar -xvf Python-2.6.6.tar
    cd Python-2.6.6
    ./configure --prefix=/home/kevet/bin/pkg/ --exec-prefix=/home/kevet/bin/pkg
    make
    make install
    export PATH="/home/kevet/bin/pkg/bin:$PATH"
   
2.    Install by python2.6
    Scipy Numpy Biopython

3.    Install Muscle / blast / Rate4 / DSSP / CDhit

4.  Rename the source directory in setup file : "single_seq_rate4site.ini"

5.  Run python2.6 1_parsepdb_557_consider_whole_chains_case_heavy_bu_normal.py 1CRN_A Y

    Y: mean to calculate the conservation values

6.    Final data find in folder PDB " 1CRNA.profile_chs "

7.    Field mean: code - 1_parsepdb_557_consider_whole_chains_case_heavy_bu_normal.py - line 917




PS.  mac 安裝 rate4site

gunzip Rate4Site.tar.gz   
tar -xvf Rate4Site.tar   
g++ -o r4s.exe -O3 -ftemplate-depth-250 *.cpp

ps. Server run

kevet@c-105:~/ConSurf$ python2.6 1_parsepdb_557_consider_whole_chains_case_heavy_bu_normal.py 1BGA_A Y

1BGA_A

 !!! Residue ARG  448 A has  8 instead of expected   7 sidechain atoms.
     last sidechain atom name is  OXT
     calculated solvent accessibility includes extra atoms !!!

 !!! HEADER-card missing !!!
 !!! COMPOUND-card missing !!!
 !!! SOURCE-card missing !!!
 !!! AUTHOR-card missing !!!
447
447
447
1788
main::logevent() called too early to check prototype at single_seq_rate4site.pl line 144.
[START] --------------------------------------------------------
[START] single_seq_rate4site version 1.0 starting...
[INFO] blasting database #1. minimum clusters: 5
[INFO] blast #1: cmd line: /home/kevet/ConSurf/ncbi-blast-2.2.25+/bin/psiblast -query pdb/1BGA/A/1BGAA.fasta -out pdb/1BGA/A/seq.blast -db /temp/db/nr -num_iterations 3 -out_ascii_pssm pdb/1BGA/A/seq.pssm -evalue 0.001 -num_threads 4 -num_descriptions 4000 -num_alignments 4000 1>>/home/kevet/ConSurf/pdb/1BGA/A/single_seq_rate4site.log 2>>/home/kevet/ConSurf/pdb/1BGA/A/single_seq_rate4site.log'
[INFO] blast #1: done
[INFO] blast #1: blast round 3 saved to 'pdb/1BGA/A/seq_last_round.blast'
[INFO] blast #1: choosing homologs from blast
[INFO] blast #1: 4117 homologs chosen from blast result
[INFO] blast #1: screen homolougs by redundancy rate, according to clusters/home/kevet/ConSurf/cd-hit-v4.5.4-2011-03-07/
[INFO] blast #1: 2142 homolog clusters found by cd-hit.
[INFO] building final sequences file 'seq_final.fasta'
[INFO] running MUSCLE, command line: '/home/kevet/ConSurf/muscle3.8.31_i86linux64 -in pdb/1BGA/A/seq_final.fasta -out pdb/1BGA/A/msa.aln -clwstrict -quiet 1>>/home/kevet/ConSurf/pdb/1BGA/A/single_seq_rate4site.log 2>>/home/kevet/ConSurf/pdb/1BGA/A/single_seq_rate4site.log'
[INFO] running rate4site, command line: /home/kevet/ConSurf/rate4site.3.2.source/rate4site -s msa.aln -o r4s.res -a 1BGAA -bn 1>rate4site_stdout.txt
Optimizing branch lengths and alpha...

likelihoodComputation::getLofPos: likelihood of pos was zero!
rate4site: errorMsg.cpp:40: static void errorMsg::reportError(const std::string&, int): Assertion `0' failed.
sh: line 1:  9243 Aborted                 /home/kevet/ConSurf/rate4site.3.2.source/rate4site -s msa.aln -o r4s.res -a 1BGAA -bn >rate4site_stdout.txt
[WARNING] error found in rate4site: likelihoodComputation::getLofPos: likelihood of pos was zero!

[WARNING] rate4site output file is empty
[INFO] running rate4site SLOW version, command line: /home/kevet/ConSurf/rate4site.3.2.source/rate4site_slow -s msa.aln -o r4s.res -a 1BGAA -bn 1>rate4site_stdout.txt
Optimizing branch lengths and alpha...
Computing the rates...
[INFO] Done :)
[END]
[END]   Run Time           : 0h 54m 58s