Dear Staff,
Thank you very much for I-TASSER.
When I tried to run new library from PDB files of 10 protein templates of my interest, I succeeded in generating template profiles using generate_profile.pl, but failed to run runI-TASSER.pl using this library.
When I would like to use only 10 protein templates without combining these templates and I-TASSER library by add_profile_to_lib.pl, how do I get the code to function properly?
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Here is the command & the wrong information for example PDB in update_IT_lib/pdb:
>>>>>>>>>>>>>>>>>>>>>>>
generate_profile.pl -blastdir '/home/XXXXXX/I-TASSER4.2/blast' -nrdir '/home/XXXXXX/ITLIB/nr' -pkgdir '/home/XXXXXX/update_IT_lib' -newdir '/home/XXXXXX/newdir' -PDBdir '/home/XXXXXX/pdb' -list list
runI-TASSER.pl -pkgdir '/home/XXXXXX/I-TASSER4.2' -libdir '/home/XXXXXX/newdir' -seqname 4U65 -datadir '/home/XXXXXX/datademo' -java_home /usr/ -light true -hours 7 -outdir '/home/XXXXXX/datademo'
1. Prepare list...
Number of templates in list: 2
2. Check PDB file...
Number of templates to be added: 2
3. Generate AAA.seq and AAA.sec...
4u65A
4u65E
4. Generate profiles for non-homologous chains...
DEP for 1/2, 4u65A
DEP for 2/2, 4u65E
MTX for 1/2, 4u65A
MTX for 2/2, 4u65E
CNT for 1/2, 4u65A
CNT for 2/2, 4u65E
SIG
1 4u65A.pdb
2 4u65E.pdb
dotProfile for 1/2, 4u65A
dotProfile for 2/2, 4u65E
stride for 1/2, 4u65A
sh: 1: /home/XXXXXX/update_IT_lib/stride: not found
stride for 2/2, 4u65E
sh: 1: /home/XXXXXX/update_IT_lib/stride: not found
5. AAA.*...
6 Check update...
checking library...
Cheers! Template profiles were generated successfully!
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runI-TASSER.pl -pkgdir '/home/XXXXXX/I-TASSER4.2' -libdir '/home/XXXXXX/newdir' -seqname 4U65 -datadir '/home/XXXXXX/datademo' -java_home /usr/ -light true -hours 7 -outdir '/home/XXXXXX/datademo'
Your setting for running I-TASSER is:
-pkgdir = /home/XXXXXX/I-TASSER4.2
-libdir = /home/XXXXXX/newdir
-java_home = /usr/
-seqname = 4U65
-datadir = /home/XXXXXX/datademo
-outdir = /home/XXXXXX/datademo
-runstyle = serial
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 5
-light = true
-hours = 7
-LBS = false
-EC = false
-GO = false
Your library files are not complete, please download library with the script download_lib.pl