Recent comments

  • Reply to: Fragment Picking with Chemical Shift Data   4 months 2 weeks ago

    This problem can arise when the input .tab file is in a different format than expected. Please see the File formats under CS Rosetta Manual

  • Reply to: 3 Steps to a CS-Rosetta structure   4 months 2 weeks ago

    Hi,

    The (Re-)Scoring of Structures link is now updated.

  • Reply to: Download and Installation   3 years 2 months ago

    For quick setup and methods testing, simply run install.py with the -nopicking option.
    This bypasses installation of the VALL and genome databases and greatly reduces the size (and time) of the installation.

    Chemical shift-based fragments can be also made using the Robetta Fragment Server:
    http://robetta.bakerlab.org/fragmentsubmit.jsp

  • Reply to: Fragment Picking with Chemical Shift Data   5 years 1 month ago

    Hello, I have install the cs-rosetta. When I run the command pick_fragments -cs ntd_trim.tab >& pick.log, I got following errors in log file and no fragment files generated.

    Expecting TALOS VERSION: post_2012
    Command: bash talos.script
    Finished running command: bash talos.script
    Error: expected creation of ntd_trim.fasta.talos/predSS.tab after running 'bash talos.script'!
    Command: /data2/csrosetta3/frag_picker/blast/bin/blastpgp -t T -i ntd_trim.fasta -F F -j2 -o ntd_trim.fasta.blast -d /data2/csrosetta3/frag_picker/genomes//nr -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C ntd_trim.fasta.chk -Q ntd_trim.fasta.pssm -a4
    /data2/csrosetta3/frag_picker/blast/bin/blastpgp: 1: ELF: not found
    /data2/csrosetta3/frag_picker/blast/bin/blastpgp: 1: @@˜*g@8: not found
    /data2/csrosetta3/frag_picker/blast/bin/blastpgp: 2: Syntax error: ")" unexpected
    Couldn't open ntd_trim.fasta.chk for reading.
    Finished running command: /data2/csrosetta3/frag_picker/blast/bin/blastpgp -t T -i ntd_trim.fasta -F F -j2 -o ntd_trim.fasta.blast -d /data2/csrosetta3/frag_picker/genomes//nr -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C ntd_trim.fasta.chk -Q ntd_trim.fasta.pssm -a4
    Error: expected creation of ntd_trim.fasta.chk after running '/data2/csrosetta3/frag_picker/blast/bin/blastpgp -t T -i ntd_trim.fasta -F F -j2 -o ntd_trim.fasta.blast -d /data2/csrosetta3/frag_picker/genomes//nr -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C ntd_trim.fasta.chk -Q ntd_trim.fasta.pssm -a4'!
    ---------------------------------------------------------------------------
    --------- CS-Rosetta 3.0 (toolbox) -----------
    ----- -----
    -- website: www.csrosetta.org --
    -- copyright: Oliver Lange --
    -- Reference: Lange et al. PNAS 2012, --
    -- www.pnas.org/cgi/doi/10.1073/pnas.1203013109 --
    -- --
    -- program name: pick_fragments --
    -- --
    ----- -----
    -------- -------
    ---------------------------------------------------------------------------
    Run TALOS+...

    Anyone can help? Thanks,

    Xiaogang

  • Reply to: 3 Steps to a CS-Rosetta structure   5 years 3 months ago

    Hi Brinda,

    the flag -nohom should be enough do remove these sequences, but there is currently a bug in the fragment picker, which will be removed with the next release.

    For now some useful commands to check and remove manually:
    The file t000_.fasta.homologous is already generated by the fragment picker and should be found in the directory with your fragments:

    write the following lines to a script: 'homs_grep.sh'
    #!/bin/bash
    frags=$1
    homs=$2
    cat $frags | gunzip | egrep "$( cat $homs | awk '{print $NF}' | sed 's/\(....\)\(.\)/\1 \2/ ' | awk '{printf("%s\\ %s|",$1,$2)}' | sed 's/|$//' )" | cut -f 2 -d " " | uniq

    # then this command shows you the homologous that still appear in your fragments.
    $ hom_grep.sh t000_.fasta.frags9.gz t000_.fasta.homologous

    write the following lines to a script 'remove_homs.sh'
    #!/bin/bash
    frags=$1
    homs=$2
    cat $frags | gunzip | egrep -v "$( cat $homs | awk '{print $NF}' | sed 's/\(....\)\(.\)/\1 \2/ ' | awk '{printf("%s\\ %s|",$1,$2)}' | sed 's/|$//' )" | gzip > $(basename $frags .gz)_nohom.gz

    # then this command should generate a new fragment file without any homs
    $ remove_homs.sh 000_.fasta.frags9.gz t000_.fasta.homologous