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pyrosetta docking script not reading/finding pdb files

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pyrosetta docking script not reading/finding pdb files
#1

Hi:  working with the D100_Docking.py script, have got past several errors but now stuck on this 

 

root@ebe6d1a96d89:/opt/PyRosetta4.Release.python36.ubuntu.release-213# ls
D100_Docking.py                 demo                rosetta       version.json
PyMOL-RosettaServer.py          full81q1.clean.pdb  self-test.py
PyMOL-RosettaServer.python3.py  full81q1.pdb        setup
apps                            pyrosetta           test
root@ebe6d1a96d89:/opt/PyRosetta4.Release.python36.ubuntu.release-213# python3 ./D100_Do
cking.py --pdb_filename 1TOH.pdb --jobs=1000 --job_output 1TOH_docking_output --translat
ion 3 --rotation 8                   
./D100_Docking.py:90: UserWarning: Import of 'rosetta' as a top-level module is deprecat
ed and may be removed in 2018, import via 'pyrosetta.rosetta'.
 from rosetta import *
core.init: Checking for fconfig files in pwd and ./rosetta/flags  
core.init: Rosetta version: PyRosetta4.Release.python36.ubuntu r213 2019.10+release.fd1b
dffb01b fd1bdffb01b7866da84942b9bf1b06e96270656e http://www.pyrosetta.org 2019-03-05T15:
28:05
core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /opt/PyRosetta4.Rele
ase.python36.ubuntu.release-213/pyrosetta/database
core.init: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111
core.init.random: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.
Created 696 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.630071 seconds.
core.import_pose.import_pose: [ ERROR ] File: 1TOH.pdb not found!

ERROR: Cannot open file "1TOH.pdb"                                                       
ERROR:: Exit from: /scratch/benchmark/W.glass/rosetta.Glass/_commits_/main/source/src/co
re/import_pose/import_pose.cc line: 350                                                  
BACKTRACE:                                                                               
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x4882b73) [0x
7f492a798b73]                                                                            
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x618295b) [0x
7f492c09895b]                                                                            
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x4857c9e) [0x
7f492a76dc9e]                                                                            
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x4856177) [0x
7f492a76c177]                                                                            
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x48548aa) [0x
7f492a76a8aa]                                                                            
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x8e59d44) [0x
7f492ed6fd44]                                                                            
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x65d62f1) [0x
7f492c4ec2f1]                                                                            
python3() [0x5030d5]                                                                     
python3(_PyEval_EvalFrameDefault+0x449) [0x506859]                                       
python3() [0x504c28]                                                                     
python3() [0x502540]                                                                     
python3() [0x502f3d]                                                                     
python3(_PyEval_EvalFrameDefault+0x449) [0x506859]                                       
python3() [0x504c28]                                                                     
python3(PyEval_EvalCode+0x23) [0x506393]                                                 
python3() [0x634d52]                                                                     
python3(PyRun_FileExFlags+0x9a) [0x634e0a]                                               
python3(PyRun_SimpleFileExFlags+0x188) [0x6385c8]                                        
python3(Py_Main+0x57a) [0x63915a]                                                        
python3(main+0xe0) [0x4a6f10]                                                            
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f4942b23b97]                 
python3(_start+0x2a) [0x5afa0a]                                                          
Traceback (most recent call last):                                                       
 File "./D100_Docking.py", line 361, in <module>
   jobs, job_output)
 File "./D100_Docking.py", line 127, in sample_docking
   pose_from_file(pose, pdb_filename)
RuntimeError:  

File: /scratch/benchmark/W.glass/rosetta.Glass/_commits_/main/source/src/core/import_pos
e/import_pose.cc:350
[ ERROR ] UtilityExitException
ERROR: Cannot open file "1TOH.pdb"


root@ebe6d1a96d89:/opt/PyRosetta4.Release.python36.ubuntu.release-213#

 

I have tried a variety of pdb files, and pdb files I ran a clean script on also.  Thanks in advance for any input!  - Amy

 

root@ebe6d1a96d89:/opt/PyRosetta4.Release.python36.ubuntu.release-213# ls
1TOH.pdb                        apps                pyrosetta     test
D100_Docking.py                 demo                rosetta       version.json
PyMOL-RosettaServer.py          full81q1.clean.pdb  self-test.py
PyMOL-RosettaServer.python3.py  full81q1.pdb        setup
root@ebe6d1a96d89:/opt/PyRosetta4.Release.python36.ubuntu.release-213#

 

Category: 
Post Situation: 
Tue, 2019-04-30 09:21
Amy F

Could you provide another set of logs from the second time you run the command:

python3 ./D100_Docking.py --pdb_filename 1TOH.pdb --jobs=1000 --job_output 1TOH_docking_output --translation 3 --rotation 8

 

The error you originally had was that the file 1TOH.pdb wasn't in the directory that you were working in.

 core.import_pose.import_pose: [ ERROR ] File: 1TOH.pdb not found!

ERROR: Cannot open file "1TOH.pdb"                                                       

 

 root@ebe6d1a96d89:/opt/PyRosetta4.Release.python36.ubuntu.release-213# ls
D100_Docking.py                 demo                rosetta       version.json
PyMOL-RosettaServer.py          full81q1.clean.pdb  self-test.py
PyMOL-RosettaServer.python3.py  full81q1.pdb        setup
apps                            pyrosetta           test

but then later you posted

 root@ebe6d1a96d89:/opt/PyRosetta4.Release.python36.ubuntu.release-213# ls
1TOH.pdb                        apps                pyrosetta     test
D100_Docking.py                 demo                rosetta       version.json
PyMOL-RosettaServer.py          full81q1.clean.pdb  self-test.py
PyMOL-RosettaServer.python3.py  full81q1.pdb        setup

where the file was there so I'm slightly confused :/

 

Tue, 2019-04-30 09:56
danpf

the file was there  (should have been there anyway!) all along, ls showed it when I rechecked it ; I have tried this on a number of pdb files.  thanks!  - Amy

Tue, 2019-04-30 10:07
Amy F

Actually... looking deeper...

Try supplying the full name of the pdb file in your commandline (make sure you use an O or a 0 (zero), correctly -- I can't tell what it is on this forums font)

ie

/opt/PyRosetta4.Release.python36.ubuntu.release-213/1TOH.pdb

 

For some reason the script moves you to a new directory on the line

import os; os.chdir('.test.output')

 

not really sure why.  once you're in .test.output the script wont be able to 'see' your files. (they will now be '../1TOH.pdb'

you can also remove the os.chdir bit if you like and are feeling adventurous . (I'm not sure of the consequences of that)

 

you can also try 'ls -la' to see if the folder .test.output even exists.

 

I'm looking at https://graylab.jhu.edu/pyrosetta/downloads/scripts/demo/D100_Docking.py

Hopefully that matches the python script you are using.

 

 

Tue, 2019-04-30 12:02
danpf