Hi Eric Thanks for getting back to me. I’m just trying to save a .py file. Not sure how to save a compressed version… I’ve tried saving in different directories, but that didn’t work either. The session contains 5 PDB files and a single .mrc file (a low resolution EM dataset). The PDB files are 5 ~40 kDa proteins, so not huge. The disk I’m writing to has ~140 GB free out of 500. Sounds like one of those elusive problems… Please let me know if you’d like me to try anything else. Best regards Joel ------------------------------------------------------------------------------------------------------------------------------ Professor Joel Mackay | NHMRC Senior Research Fellow Chair, Biochemistry, Cellular and Molecular Biology Cluster School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay E: joel.mackay@sydney.edu.au | W: www.mmb.usyd.edu.au/mackay/ From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Friday, 11 August 2017 6:55 AM To: Joel Mackay <joel.mackay@sydney.edu.au> Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Error in Windows saving a session Hi Joel, We have had this reported infrequently by other users and have had no success in tracking it down. Can you answer a couple of questions for me? Are you writing a compressed session file? Is the disk you are writing to nearly full? Thanks. —Eric Eric Pettersen UCSF Computer Graphics Lab On Aug 9, 2017, at 2:45 AM, Joel Mackay <joel.mackay@sydney.edu.au<mailto:joel.mackay@sydney.edu.au>> wrote: Hi all Have other people seen (and solved!) this error before (below)? I’m having it crop up pretty much all the time now when I try to save a session (on my Win7 machine – running Chimera 1.11.2. Thanks Joel WindowsError Exception in Tk callback Function: <function command at 0x00000000155434A8> (type: <type 'function'>) Module: <module 'chimera.baseDialog' from 'C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.pyc'> (line: 447) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 264, in Save getattr(self, self.keepEquiv())() File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 704, in OK self.Apply() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 183, in Apply self.command(1, self) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\gui.py", line 41, in _saveCB saveSession(paths[0], **kw) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) WindowsError: [Error 32] The process cannot access the file because it is being used by another process WindowsError: [Error 32] The process cannot access the file because it is being used by another process File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) See reply log for Python traceback. ------------------------------------------------------------------------------------------------------------------------------ Professor Joel Mackay | NHMRC Senior Research Fellow Chair, Biochemistry, Cellular and Molecular Biology Cluster School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay E: joel.mackay@sydney.edu.au<mailto:joel.mackay@sydney.edu.au> | W: www.mmb.usyd.edu.au/mackay/<http://www.mmb.usyd.edu.au/mackay/> _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

No joy ------------------------------------------------------------------------------------------------------------------------------ Professor Joel Mackay | NHMRC Senior Research Fellow Chair, Biochemistry, Cellular and Molecular Biology Cluster School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay E: joel.mackay@sydney.edu.au | W: www.mmb.usyd.edu.au/mackay/ From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Saturday, 12 August 2017 3:04 AM To: Joel Mackay <joel.mackay@sydney.edu.au> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Error in Windows saving a session Could you try rebooting your machine? —Eric On Aug 10, 2017, at 4:44 PM, Joel Mackay <joel.mackay@sydney.edu.au<mailto:joel.mackay@sydney.edu.au>> wrote: Hi Eric Thanks for getting back to me. I’m just trying to save a .py file. Not sure how to save a compressed version… I’ve tried saving in different directories, but that didn’t work either. The session contains 5 PDB files and a single .mrc file (a low resolution EM dataset). The PDB files are 5 ~40 kDa proteins, so not huge. The disk I’m writing to has ~140 GB free out of 500. Sounds like one of those elusive problems… Please let me know if you’d like me to try anything else. Best regards Joel ------------------------------------------------------------------------------------------------------------------------------ Professor Joel Mackay | NHMRC Senior Research Fellow Chair, Biochemistry, Cellular and Molecular Biology Cluster School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay E: joel.mackay@sydney.edu.au<mailto:joel.mackay@sydney.edu.au> | W: www.mmb.usyd.edu.au/mackay/<http://www.mmb.usyd.edu.au/mackay/> From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Friday, 11 August 2017 6:55 AM To: Joel Mackay <joel.mackay@sydney.edu.au<mailto:joel.mackay@sydney.edu.au>> Cc: chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Error in Windows saving a session Hi Joel, We have had this reported infrequently by other users and have had no success in tracking it down. Can you answer a couple of questions for me? Are you writing a compressed session file? Is the disk you are writing to nearly full? Thanks. —Eric Eric Pettersen UCSF Computer Graphics Lab On Aug 9, 2017, at 2:45 AM, Joel Mackay <joel.mackay@sydney.edu.au<mailto:joel.mackay@sydney.edu.au>> wrote: Hi all Have other people seen (and solved!) this error before (below)? I’m having it crop up pretty much all the time now when I try to save a session (on my Win7 machine – running Chimera 1.11.2. Thanks Joel WindowsError Exception in Tk callback Function: <function command at 0x00000000155434A8> (type: <type 'function'>) Module: <module 'chimera.baseDialog' from 'C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.pyc'> (line: 447) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 264, in Save getattr(self, self.keepEquiv())() File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 704, in OK self.Apply() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 183, in Apply self.command(1, self) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\gui.py", line 41, in _saveCB saveSession(paths[0], **kw) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) WindowsError: [Error 32] The process cannot access the file because it is being used by another process WindowsError: [Error 32] The process cannot access the file because it is being used by another process File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) See reply log for Python traceback. ------------------------------------------------------------------------------------------------------------------------------ Professor Joel Mackay | NHMRC Senior Research Fellow Chair, Biochemistry, Cellular and Molecular Biology Cluster School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay E: joel.mackay@sydney.edu.au<mailto:joel.mackay@sydney.edu.au> | W: www.mmb.usyd.edu.au/mackay/<http://www.mmb.usyd.edu.au/mackay/> _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

Hi Tracy, Yes, here’s what we think is happening. When Chimera writes out a session file, it writes it out to a temporary file and then moves that file to the desired final name. It does this to prevent destroying an older, good session file if there is some error encountered while saving the new session. So, the “file with an odd name” that you saw is the temporary file. Chimera wrote that out successfully and that’s why it worked when you opened it. The problem is that between the time it finished writing the file and the time it tried to move it to the final name (which isn’t much time!) some program running on your machine started reading it, resulting in the error message about “being used by another process”. Now, we don’t really know what the other mystery process is. it is most likely a virus scanner or some other security software that looks a every new file created on your machine. If that rings any bells, perhaps you can configure the problematic program to not try to scan files with a .py suffix… —Eric Eric Pettersen UCSF Computer Graphics Lab

On Apr 19, 2018, at 3:26 PM, Tracy Nixon <btn1@psu.edu> wrote:

Hi Joel,

I noticed I have a similar problem as you posted using Chimera on Windows, with saving a session giving the error:

WindowsError: [Error 32] The process cannot access the file because it is being used by another process

In my case, using win10 and the current chimera as of today, the program writes out a file that is of odd name, even though I get the error message.

If I simply rename the file to something.py and open it from Chimera it works as it should.

Sincerely,

Tracy

-- B. Tracy Nixon Professor of Biochemistry and Molecular Biology 332 S. Frear Lab Penn State University University Park, PA 16802 USA 814 863 4904 (office) 814 777 1091 (cell) 814 863 7024 (fax) btn1@psu.edu (email) http://bmb.psu.edu/directory/btn1 (web)

bmb.psu.edu/graduate/how-to-apply huck.psu.edu/education/molecular-cellular-and-integrative-biosciences **NEW PROGRAM!**

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