In csrosetta, there are several scripts to convert files to another format
bmrb2fasta GmR137.bmrb > ../expected_outputs/bmrb2fasta.fasta bmrb2prot GmR137.bmrb -start 1 -end 30 > ../expected_outputs/bmrb2prot.prot bmrb2talos GmR137.bmrb > ../expected_outputs/bmrb2talos.tab talos2bmrb gmr137.tab > ../expected_outputs/talos2bmrb.bmrb talos2fasta gmr137.tab > ../expected_outputs/talos2fasta.fasta talos2prot gmr137.tab > ../expected_outputs/talos2prot.prot pdb2fasta native.pdb > ../expected_outputs/pdb2fasta.fasta prot2talos gmr137.prot > ../expected_outputs/prot2talos.tab
Attachment is an example of this tutorial. It includes all the inputs and outputs.
Comments
greenfur
Fri, 06/29/2012 - 05:11
Permalink
error messages for the first three scripts (help)
File "/home/greenfur/Softwares/csrosetta3/com_alias/bmrb2talos", line 72, in
(fasta, fastas, nmol)=bmrb.get_sequence( bmrb_file )
File "/home/greenfur/csrosetta3/python/bmrb.py", line 244, in get_sequence
seq_frames=bmrb_file._frames['monomeric_polymer']
KeyError: 'monomeric_polymer'
olange
Sat, 06/30/2012 - 13:12
Permalink
problems with BMRB file conversion
Hi Greenfur,
unfortunately the BMRB format is not highly standardized. It seems the frame 'monomeric_polymer' is missing. Could
you send me your BMRB file and I will work on making the reader more flexible for other cases.
Best,
Oliver
greenfur
Sat, 06/30/2012 - 17:24
Permalink
problems with BMRB file conversion
Thank you very much, Oliver.
I was actually working with the files downloaded from your tutorial. The file is "gmr137.prot". I noticed that for some unknown reason it became an empty file when I was playing with those file conversion commands (somehow I screwed it up). After I unzip the "file_conversion.tgz" again, everything is fine.
May I suggest you to add some instruction to your toolbox installation guide?
In the file "bmrb2fasta.py" and others, there are several sentences like "from ExampleArgumentParser import ExampleArgumentParser" and "import bmrb". It seems that one has to manually add "source /home/greenfur/Softwares/csrosetta3/com/init.bashrc" to the .bashrc file to make those modules importable.
Again, thank you for your help.
olange
Sat, 06/30/2012 - 18:40
Permalink
source com/init
Hi Greenfur,
"It seems that one has to manually add "source /home/greenfur/Softwares/csrosetta3/com/init.bashrc" to the .bashrc file to make those modules importable. "
the point has already been made in 2.4 of the installation guide.
I'll print it in bold now to make it more visible.
Best,
Oliver