pyrosetta docking script not reading/finding pdb files

This topic has 3 replies, 2 voices, and was last updated 5 years, 7 months ago by Anonymous.

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- April 30, 2019 at 4:21 pm #3130
  Anonymous
  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#
- April 30, 2019 at 4:56 pm #14692
  Anonymous
  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
  - April 30, 2019 at 5:07 pm #14693
    Anonymous
    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
- April 30, 2019 at 7:02 pm #14694
  Anonymous
  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.
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