- This topic has 7 replies, 3 voices, and was last updated 11 years ago by Anonymous.
November 12, 2012 at 3:31 am #1460Anonymous
Run on cluster
I’m attempting to setup rosetta antibody but encounter the error message below( script ram_buildloop_wrapper4.pl is missing).
My installation is rosetta 2.3.0. The script doesn’t seem to be in rosetta++ or rosetta3 either.
[…@login-0-0 test]$ perl -P ../antibody/scripts/ram_buildloop_wrapper4.pl ../antibody/database/pdb1xyz_chothia.pdb bit ram ram 1 1 1 1 1 0 0 1 1 0 0 0 0 FR 02 2 1 3 2000 2000 3 0 ../1dqq_h.fasta 1dqq_l.fasta
Can’t open /home/…/immunity/antibody/scripts/ram_create_query_fasta.pl: No such file or directory.
These are the contents of the script directory:
[…@login-0-0 scripts]$ ls
build ram_assignnumbering.pl ram_create_query_database.pl ram_print_residues_fromfasta.pl
fasta.blast ram_blankcdrs.pl ram_create_rmsd_table_h3frags.pl ram_profit_script_h3frags.pl
get_cterm_residues.pl ram_blastscript_h3frag.pl ram_id_perfect_matches.pl ram_profit_script.pl
get_mer_from_fasta.pl ram_blastscript.pl ram_kink_query.pl ram_read_matches.pl
getminimum_per_identity.pl #ram_buildloop_wrapper4.pl# ram_make_rosetta_fragments.pl ram_setup_rrun2.pl
make_rosetta_fragments.pl ram_buildloop_wrapper4.pl ram_mapping1.pl readdsspline.pl
paths.txt ram_cluster_h3frags.pl ram_match_hacks.pl read_h3pseudodihedral.pl
pdb_cleaner.pl ram_copytemplates1.pl ram_members_of_list.pl readinfo.pl
ram_analyze_blast8.pl ram_create_condor_script.pl ram_mutate_pdb2.pl readpdbline.pl
ram_analyze_blast_h3frag.pl ram_create_H3CterNter2.pl #rampaths.txt# removespaces.pl
ram_append_abfrags_to_rosettafrags2.pl ram_create_query_database_lightheavy.pl rampaths.txt utilities.txt
November 12, 2012 at 4:17 am #8073Anonymous
Linux version 2.6.18-238.19.1.el5xen
(email@example.com) (gcc version 4.1.2 20080704 (Red
Hat 4.1.2-50)) #1 SMP Sun Jul 10 09:02:57 EDT 2011
OS type: Redhat Enterprise Linux (A guess because it is common, the “el”
at the end of the kernel version ID, and the redhat address/compiler.)
November 12, 2012 at 4:52 pm #8074Anonymous
I moved your post into the ++ directory.
Your ls operation clearly shows the existence of both ram_buildloop_wrapper4.pl and its emacs autosave #ram_buildloop_wrapper4.pl# – I don’t understand why you say it isn’t present.
November 12, 2012 at 8:36 pm #8078Anonymous
Hi, you are supposed to need “ram_buildloop_wrapper.pl” file, I am not sure why you were asked to use “ram_buildloop_wrapper4.pl”. But anyway, please checkout a version in the trunk: https://svn.rosettacommons.org/source/trunk/antibody You can find the instructions in the “antibody_readme.txt” file, and the example in the “antibody_examples.tgz” file. Please realize that you need rosetta++ executable to run the scripts. “scripts.v2” is the new version that we are working on and will be realized in the near future.
November 14, 2012 at 2:33 pm #8092Anonymous
The missing file is “ram_create_query_fasta.pl”.
ram_buildloop_wrapper.pl is the file from Rosetta 3.* (which also refers
to the missing file “ram_create_query_fasta.pl”)
ram_buildloop_wrapper4.pl is the the file from Rosetta++
Also, is Rosetta 3.* stable enough for usage with the
Antibody package, because both scripts refer to ram_create_query_fasta.pl
November 12, 2012 at 8:49 pm #8079Anonymous
jchin is an academic user and has access only to the released code (he specified the 2.3.0 release). You can see the release he has a copy of at https://svn.rosettacommons.org/trac/browser/branches/releases/rosetta-2.3.0, but he can’t get to SVN.
November 14, 2012 at 2:51 pm #8093Anonymous
I tried to pull you a copy of “ram_create_query_fasta.pl” from trunk as Jianqing suggested – unfortunately it isn’t there! Hopefully he can find it.
November 14, 2012 at 4:07 pm #8094Anonymous
Hi. I checked the scripts. The “ram_create_query_fasta.pl” is not available, but it is not useful anyway. What it is supposed to do is to get antibody sequence from an input PDB, and saved into two fasta files. However, The default of the script assumes you have two fasta files (light and heavy) ready and will be read and used directly. If you check the “ram_buildloop_wrapper.pl”, you will find this line “system2(“perl -P $scripts/ram_create_query_fasta.pl $pdb $chainL $chainH” ) if ( $pdb_input ) ;” and this $pdb_input is hardcoded to be 0. In a word, you don’t need this file, at least for the version of the script in the trunk.
The antibody scripts in Rosetta 3.* still use Rosetta++ executable, except camelid antibodies. I know it is weird… and we are upgrading it … but in any cases, if you will work on regular antibodies, just use the scripts in Rosetta 3.* and use the executable in Rosetta 2.*
The complete new RosettaAntibody homology modeling is expected to be release the end of the year or the beginning of next year.
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