Kortemme-Lab sequence-tolerance issues

Kortemme-Lab / sequence-tolerance

A sequence tolerance benchmark capture containing the benchmark dataset and benchmarked protocol captures.

https://kortemmelab.ucsf.edu/benchmarks

MIT License

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issues

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The output files of backrub_seqtol.py end up in settings.json:"output_dir" not WORKING_DIRECTORY

#22 momeara opened 9 years ago
0
indicate 'cp settings.json.example settings.json' is necessary

#21 momeara opened 9 years ago
0
Indicate in the backrub_seqtol protocol how long the protocol takes

#20 momeara opened 9 years ago
4
The analysis README.rst is missing a section on how to interpret the results

#19 momeara opened 9 years ago
1
Can the data folder be removed? If not indicate how it should be used

#18 momeara closed 9 years ago
1
I'm confused how backrub_seqtol.py and seqtol_resfile.py fit together

#17 momeara closed 9 years ago
1
description of backrub_seqtol.py on front readme seems out of place

#16 momeara closed 9 years ago
1
In the intro, make "This benchmark includes" into a bulleted list.

#15 momeara closed 9 years ago
1
I like the Files generated for each step, but can you also include a subsection for input files as well

#14 momeara opened 9 years ago
1
Steps on first page just for testing or is this the full benchmark?

#13 momeara closed 9 years ago
1
protocols/backrub_seqtol -> Example Overall Command Line

#12 momeara closed 9 years ago
3
specify input/output files for running sequence tolerance analysis

#11 momeara closed 9 years ago
4
Running process_specificity() gives deprecation warning, use process_seqtol() instead

#10 momeara closed 9 years ago
3
Should on of output/1N7T and output/sample be removed? They look very similar...

#9 momeara closed 9 years ago
1
Fix format of command lines

#8 momeara closed 9 years ago
1
For all command lines indicate roughly how long they should take

#7 momeara closed 9 years ago
1
For all paths that the user needs to change, such as the the path to Rosetta or the rosetta database, put them in angle brackets like <path/to/rosetta>/main/source/

#6 momeara closed 9 years ago
1
Add "\" line continuation characters in command lines so they can be copied and pasted into the terminal

#5 momeara closed 9 years ago
1
Indicate the directory where the command lines should be run.

#4 momeara closed 9 years ago
1
Improve description of benchmark and outputs for benchmark

#3 momeara closed 9 years ago
1
Some of the scripts have Rosetta headers and some do not, is this a problem?

#2 momeara opened 9 years ago
1
Subtitle for project has broken link to https://kortemmelab.ucsf.edu/benchmarks

#1 momeara closed 9 years ago
2