More on File Conversion

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's picture

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'

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's picture

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.

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