I created a fragment file of my structure using Robetta, the link to the results is right here http://robetta.bakerlab.org/fragmentqueue.jsp?id=51178. I'm using the
fragment file to do density guided structure prediction as described in the paper "De novo protein structure determination from near-atomic resolution cryo-EM maps".
I'm trying to run the code below:
#!/bin/sh
mkdir round1
$ROSETTA3/source/bin/denovo_density.linuxgccrelease\
-in::file::fasta /home/labusr/Documents/tubulin_exercise/5UCY.fasta \
-fragfile ./home/labusr/Documents/tubulin_exercise/9mers\
-mapfile ./home/labusr/Documents/tubulin_exercise/masked_map_center.mrc\
-n_to_search 2000 -n_filtered 9000 -n_output 50 \
-bw 16 \
-atom_mask_min 2 \
-atom_mask 3 \
-clust_radius 3 \
-clust_oversample 4 \
-point_radius 3 \
-movestep 1 \
-delR 2 \
-frag_dens 0.8 \
-ncyc 3 \
-min_bb false \
-pos $1 \
-out:file:silent round1/tubulin.$1.silent
I'm recieving the error below, that I would appreciate if somebody helps me with.
ERROR: ERROR: FragmentIO: could not open file ./home/labusr/Documents/tubulin_exercise/9mers
ERROR:: Exit from: src/core/fragment/FragmentIO.cc line: 231
BACKTRACE:
/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libutility.so(utility::exit(std::string const&, int, std::string const&, int)+0x27f) [0x7fe4b3e2f48f]
/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::fragment::FragmentIO::read_data(std::string const&)+0xab4) [0x7fe4b832f864]
/home/labusr/rosetta/main//source/bin/denovo_density.linuxgccrelease() [0x42f70d]
/home/labusr/rosetta/main//source/bin/denovo_density.linuxgccrelease() [0x430387]
/home/labusr/rosetta/main//source/bin/denovo_density.linuxgccrelease() [0x429869]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x7fe4b1e24c05]
/home/labusr/rosetta/main//source/bin/denovo_density.linuxgccrelease() [0x429f59]
Category:
Post Situation:
You have a dot in front of the path to the file. This means that you're starting from the current directory (a "relative path"). You probably want an absolute path, which will start with just a slash.
Alternatively, if you're running it from within the /home/labusr/Documents/tubulin_exercise/ directory, you can just give the relative path to the file (e.g. './9mers')
On a different note, if you are outputting files into a directory (like you are with round1/tubulin.$1.silent) make sure the directory exists (e.g. with mkdir) prior to running Rosetta. While Rosetta can create files which don't exist yet, it won't create directories which don't exist.