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mutate_residue not working

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mutate_residue not working
#1

Dear Sir or Madam,
Can I ask how to properly use the command of
mutate_residue(pose, 49, 'E') ?

It seems to be quite straightforward as pose name, residue number and amino acids are included into the parenthesis. However, I have been told
"MemoryError" (attached) after typing

from toolbox import mutate_residue
mutate_residue(A10, 3, 'E')

Do I need to type something else before using this command?

Basically, I want to mutate several amino acids into customised ones. Is this the best way to do?

I installed PyRosetta (PyRosetta.Windows.64Bit.monolith.mode=release.branch=release-r10.exe) on my AMD 64 bit Win 7 PC. Hope this is not a problem.

Thank you very much.

Yours sincerely
Cheng

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mutate_residue.png32.85 KB
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Mon, 2014-08-11 03:55
lanselibai

A MemoryError in Python is due to there not being a sufficient amount of memory on your system - it's not a PyRosetta specific thing. As a general rule of thumb, you'll want ~1 GB of memory for each instance of Rosetta you're running (you can get away with less, depending on what you're doing, but 1 GB is recommended to be on the safe side). This is not including any of the memory allocated for other things you're running on your system. So if you were trying to run PyRosetta on an older system where you also had Word and your browser and Powerpoint and email client and Excel and PyMol and iTunes (and ...) open, I'd recommend closing all of the programs you don't immediately need and try running things again.

Tue, 2014-08-12 08:32
rmoretti

Hi rmoretti,
Thank you very much for your help. I am using AMD Dual-Core 2.30 GHz Processor with RAM 4.00 GB. Maybe it is too old now.

I closed the other programmes as many as possible before running again. However, my PC was freezing for more than 30 min. So I restart it again.
Can I ask do you use PyRosetta on your personal PC, or on a cluster?

I have followed Sergey's instructions and attached the test reports in another reply.

Thank you.

Yours sincerely
Cheng

Wed, 2014-08-13 07:39
lanselibai

Hi Cheng,

Could you please try running 'PyRosetta Self Tests' from the start menu and see if all tests pass? (if you used installer this start-item should be created for you)

One of the test (test/Workshop6test.py in PyRosetta install location) is demo file which illustrate of how to use mutate_residue function. As Rocco mentioned it could be that your system just does not have enough memory (and by running build-in test i am trying to determent if that the case). You can also just run one test (Workshop6test.py) instead of whole test suite.

Thanks,

Tue, 2014-08-12 21:42
Sergey

Hi Sergey,
Many thanks for your help! I have run both 'PyRosetta Self Tests' and 'Workshop6test.py'. The attachments are their screenshots. Unfortunately, they seem to fail the tests.

For the 'PyRosetta Self Tests', what is the meaning of "cp is not recognized as an internal or external command"?

For the 'Workshop6test.py', I can confirm the file of "1YY8.clean.pdb" does exist in the directory (attached).

Could you please help me ? Thank you very much.

Yours sincerely
Cheng

Wed, 2014-08-13 06:46
lanselibai

"cp" is the Unix & Mac way of copying files - it's sometimes also recognized on Windows, depending on your settings. The error message just means that the PyRosetta Self Tests aren't written to be maximally compatible with all Windows installations - it doesn't necessarily imply anything about your problems. I believe you can substitute the "copy" command for "cp", if you want to manually re-run the commands from the self-test.

The 1YY8.clean.pdb issue is due to current working directory issues. It's trying to open test/data/workshops/1YY8.clean.pdb, but you're already in the test/ directory, so things don't work out. Do a "cd D:\PyRosetta" in your terminal and then try "python test\Workshop6test.py" to see if that works better.

Wed, 2014-08-13 09:46
rmoretti

Hi rmoretti,
The self-test really works after changing the "cp" into "copy" as you said!

However, after running several command lines, my PC freezes for more than half an hour as shown in the attachment. I think my PC could not tolerate the heavy computing of the test. I consider switching to a cluster instead of my dual-core AMD 2.3 GHz processor on a Win 7 PC. How do you think of it?

Thank you.

Yours sincerely
Cheng

File attachments: 
Thu, 2014-08-14 03:32
lanselibai

Hi rmoretti,
I have run both "PyRosetta self test" and "Workshop6test" (attached) overnight with my own PC.

1) For "Workshop6test", it finished after one night run. The attachment is its screenshot in the end.

2) For "PyRosetta self test", 12440 command lines were generated after one night run and was not finished. So I closed it then.

I am contacting our cluster service in our university. Hopefully, I can run Pyrosetta there.

Thank you very much for your help!

Yours sincerely
Cheng

File attachments: 
Sun, 2014-08-17 07:30
lanselibai