Dear rosetta user:
I have try to learn the tutorial in electron_density/cryo_em tutorial /scenario2_close_homology/, but when I run the run2_relax_cm_inputs.sh, there is no output, and only a warning messege, say "protocols.comparative_modeling.ThreadingJobInputter: Warning: no template pdb provided for alignment ". Can any one tell me how to solve this problem, thanks a lot. The content in run2_relax_cm_inputs.sh is show as follow, and I have a file 1OJ8A.pdb in the fold.
!/bin/bash
relax.default.linuxgccdebug \
-database $rosetta_database \
-in::file::extended_pose 1 \
-in::file::fasta 1onc.fasta \
-in::file::alignment 1onc_1oj8.fasta \
-in::file::template_pdb 1OJ8A.pdb \
-relax:fast \
-relax::default_repeats 4 \
-relax::jump_move true \
-edensity::mapfile 1ONC.5A.mrc \
-edensity::mapreso 5.0 \
-edensity::grid_spacing 2.0 \
-edensity::whole_structure_ca_wt 0.1 \
-overwrite
The content of 1onc_1oj8.fasta is as follow:
onc_.pdb 1 DWLTFQKKHITNTRDVDCDNIMSTNLFHCKDKNTFIYSRPEPVKAICKGIIASKNVLTTSEFYLSDCNVTSRPCKYKLKKSTNKFCVTCENQAPVHFVGVGSC
1OJ8A.pdb 2 DWDTFQKKHLTDTKKVKCDVEMKKALFDCKKTNTFIFARPPRVQALCKNIKNNTNVLSRDVFYLPQCNRKKLPCHYRLDGSTNTICLTCMKELPIHFAGVGKC
Best regards,
This may be due to your alignment format. By default it's expecting a "grishin" formatted alignment (see https://www.rosettacommons.org/docs/latest/minirosetta-comparative-model... ) It looks like you have a "general" formatted alignment. Try adding the option "-cm:aln_format general" to the commandline.
The other thing you may want to do is output extra information to the log, so see details about what it's trying to do. Add the option "-out:level 400" to output extra debugging information (the default output level is 300)