RosettaCM Tutorials

[Anonymous]

I have been attempting to run the RosettaCM tutorial on a Linux machine. I have not been able to run the tutorial becuase the file “clean_pdb.py” in /demos/tutorials/rosetta_cm/scripts/ calls upon a file amino_acids.py that does not appear to be anywhere in the rosetta bundle I downloaded onto the machine. The path to the amino_acids.py file appears to lead to the computer of a developer. I have been able to locate a tar file containing the amino_acids.py file and thus have it on my computer, but I do not know how to gain permission to edit the path to the file in the clean_pdb.py file.

Thanks

 

[Anonymous]

you might have an older version of rosetta on your computer since rosetta 3.7 clean_pdb.py does not call upon any files as far as i can see.

I just get rid of everything except for the ATOM, HETATM lines and CM seems to work fine. try it and see.

[Anonymous]

you might have an older version of rosetta on your computer since rosetta 3.7 clean_pdb.py does not call upon any files as far as i can see.

I just get rid of everything except for the ATOM, HETATM lines and CM seems to work fine. try it and see.

[Anonymous]

you might have an older version of rosetta on your computer since rosetta 3.7 clean_pdb.py does not call upon any files as far as i can see.

I just get rid of everything except for the ATOM, HETATM lines and CM seems to work fine. try it and see.

[Anonymous]

The “official” version of clean_pdb.py for general use is at Rosetta/tools/protein_tools/scripts/clean_pdb.py and the version from a recent-ish release should work if you run it from that directory (as opposed to copying the script to the local directory before running.)

[Anonymous]

The “official” version of clean_pdb.py for general use is at Rosetta/tools/protein_tools/scripts/clean_pdb.py and the version from a recent-ish release should work if you run it from that directory (as opposed to copying the script to the local directory before running.)

[Anonymous]

The “official” version of clean_pdb.py for general use is at Rosetta/tools/protein_tools/scripts/clean_pdb.py and the version from a recent-ish release should work if you run it from that directory (as opposed to copying the script to the local directory before running.)

[Anonymous]

Whenever I vi into “clean_pdb.py” I get this.

!/dors/meilerlab/apps/Linux2/x86_64/bin/python2.5

“written by Phil Bradley, Rhiju Das, Michael Tyka, TJ Brunette, and James Thompson from the Baker Lab. Edits done by Steven Combs, Sam Deluca and Jordan Willis  from the Meiler Lab.”

import sys
import os
from sys import argv, stderr, stdout
from os import popen, system
from os.path import exists, basename
from amino_acids import longer_names
from amino_acids import modres
# remote host for downloading pdbs
remote_host = ”

shit_stat_insres = False
shit_stat_altpos = False
shit_stat_modres = False
shit_stat_misdns = False  # missing density!

fastaseq = {}
pdbfile = “”
“clean_pdb.py” [readonly] 313 lines, 9544 characters

It appears it is pulling “longer_names”  from “amino_acids.py”. I do not see ATOM, HETATM, or CM lines. Whenever I try to run the program, I get an error saying that the amino_acids.py file cannot be found and thus it cannot import “longer_names”.

 

[Anonymous]

Whenever I vi into “clean_pdb.py” I get this.

!/dors/meilerlab/apps/Linux2/x86_64/bin/python2.5

“written by Phil Bradley, Rhiju Das, Michael Tyka, TJ Brunette, and James Thompson from the Baker Lab. Edits done by Steven Combs, Sam Deluca and Jordan Willis  from the Meiler Lab.”

import sys
import os
from sys import argv, stderr, stdout
from os import popen, system
from os.path import exists, basename
from amino_acids import longer_names
from amino_acids import modres
# remote host for downloading pdbs
remote_host = ”

shit_stat_insres = False
shit_stat_altpos = False
shit_stat_modres = False
shit_stat_misdns = False  # missing density!

fastaseq = {}
pdbfile = “”
“clean_pdb.py” [readonly] 313 lines, 9544 characters

It appears it is pulling “longer_names”  from “amino_acids.py”. I do not see ATOM, HETATM, or CM lines. Whenever I try to run the program, I get an error saying that the amino_acids.py file cannot be found and thus it cannot import “longer_names”.

 

[Anonymous]

Whenever I vi into “clean_pdb.py” I get this.

!/dors/meilerlab/apps/Linux2/x86_64/bin/python2.5

“written by Phil Bradley, Rhiju Das, Michael Tyka, TJ Brunette, and James Thompson from the Baker Lab. Edits done by Steven Combs, Sam Deluca and Jordan Willis  from the Meiler Lab.”

import sys
import os
from sys import argv, stderr, stdout
from os import popen, system
from os.path import exists, basename
from amino_acids import longer_names
from amino_acids import modres
# remote host for downloading pdbs
remote_host = ”

shit_stat_insres = False
shit_stat_altpos = False
shit_stat_modres = False
shit_stat_misdns = False  # missing density!

fastaseq = {}
pdbfile = “”
“clean_pdb.py” [readonly] 313 lines, 9544 characters

It appears it is pulling “longer_names”  from “amino_acids.py”. I do not see ATOM, HETATM, or CM lines. Whenever I try to run the program, I get an error saying that the amino_acids.py file cannot be found and thus it cannot import “longer_names”.

 

[Anonymous]

I downloaded the version I have in September I believe, and it was the most recent linux release then. I downloaded “rosetta_bin_linux_2016.32.58837_bundle”. I think this version should be recent enough. What do you mean by running it from that directory instead of copying the script to the local directory? Sorry, I’m still kind of new to this stuff.

[Anonymous]

I downloaded the version I have in September I believe, and it was the most recent linux release then. I downloaded “rosetta_bin_linux_2016.32.58837_bundle”. I think this version should be recent enough. What do you mean by running it from that directory instead of copying the script to the local directory? Sorry, I’m still kind of new to this stuff.

[Anonymous]

I downloaded the version I have in September I believe, and it was the most recent linux release then. I downloaded “rosetta_bin_linux_2016.32.58837_bundle”. I think this version should be recent enough. What do you mean by running it from that directory instead of copying the script to the local directory? Sorry, I’m still kind of new to this stuff.

[Anonymous]

By “running from that directory” I mean providing the full path to the script as it exists in the main Rosetta distribution, e.g. “python ~/Rosetta/tools/protein_tools/scripts/clean_pdb.py  <arguments>”

Some people (for whatever reason) tend to first copy scripts into their working directory, and then run it from that directory (e.g. “python ./clean_pdb.py”) — this is not necessarily going to work.

Is the top of the clean_pdb.py is from the demos directory? The one in the protein_tools directory shouldn’t look like that for rosetta_bin_linux_2016.32.58837_bundle — if it does, you have an older version of Rosetta than you think.

 

[Anonymous]

By “running from that directory” I mean providing the full path to the script as it exists in the main Rosetta distribution, e.g. “python ~/Rosetta/tools/protein_tools/scripts/clean_pdb.py  <arguments>”

Some people (for whatever reason) tend to first copy scripts into their working directory, and then run it from that directory (e.g. “python ./clean_pdb.py”) — this is not necessarily going to work.

Is the top of the clean_pdb.py is from the demos directory? The one in the protein_tools directory shouldn’t look like that for rosetta_bin_linux_2016.32.58837_bundle — if it does, you have an older version of Rosetta than you think.

 

[Anonymous]

By “running from that directory” I mean providing the full path to the script as it exists in the main Rosetta distribution, e.g. “python ~/Rosetta/tools/protein_tools/scripts/clean_pdb.py  <arguments>”

Some people (for whatever reason) tend to first copy scripts into their working directory, and then run it from that directory (e.g. “python ./clean_pdb.py”) — this is not necessarily going to work.

Is the top of the clean_pdb.py is from the demos directory? The one in the protein_tools directory shouldn’t look like that for rosetta_bin_linux_2016.32.58837_bundle — if it does, you have an older version of Rosetta than you think.

 

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