Can't write PDB file

[DLMLEN001@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\Lenye\Dropbox\CynD_thermostability\Truncated_WT_CynD.pdb
> format PDB

Summary of feedback from opening
C:\Users\Lenye\Dropbox\CynD_thermostability\Truncated_WT_CynD.pdb  
---  
warnings | Ignored bad PDB record found on line 284  
  
  
Ignored bad PDB record found on line 285  
  
  
Ignored bad PDB record found on line 286  
  
  
Ignored bad PDB record found on line 287  
  
  
Ignored bad PDB record found on line 288  
  
  
25 messages similar to the above omitted  
  
Chain information for Truncated_WT_CynD.pdb #1  
---  
Chain | Description  
A | No description available  
B H J M O | No description available  
C D E G I K | No description available  
  

> show cartoons

> hide atoms

> select /K:72

15 atoms, 14 bonds, 1 model selected  

> show sel atoms

> style sel stick

Changed 15 atom styles  

> toolshed show Contacts

> contacts sel resSeparation 5 intraMol false select true dashes 3 radius 0.5
> showDist true reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Ignore contacts between atoms in residues less than 5 apart in sequence
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: False
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> select up

2 atoms, 1 bond, 1 model selected  

> ui mousemode rightMode swapaa

> swapaa mousemode /K:72 LYS

> save2 "C:/Users/Lenye/Desktop/PhD_2021/Rational protein
> engineering/H71K.pdb"

> select /K:57

20 atoms, 20 bonds, 1 model selected  

> ui mousemode rightMode swapaa

> show sel atoms

> style sel stick

Changed 20 atom styles  

> ui mousemode rightMode swapaa

> swapaa mousemode /K:57 TYR

> select /K:57@HH

1 atom, 1 model selected  

> select up

21 atoms, 21 bonds, 1 model selected  

> ui mousemode rightMode swapaa

> save2 "C:/Users/Lenye/Desktop/PhD_2021/Rational protein
> engineering/H71K/F57Y.pdb"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1373, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 90, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 101, in show_save_file_dialog  
_dlg.display(session, session.ui.main_window)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 31, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 60, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\pdb\\__init__.py", line 89, in save  
pdb.save_pdb(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\pdb\pdb.py", line 119, in save_pdb  
(serial_numbering == "h36"), polymeric_res_names)  
OSError: Unable to open file 'C:/Users/Lenye/Desktop/PhD_2021/Rational protein
engineering/H71K/F57Y.pdb' for writing  
  
OSError: Unable to open file 'C:/Users/Lenye/Desktop/PhD_2021/Rational protein
engineering/H71K/F57Y.pdb' for writing  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\pdb\pdb.py", line 119, in save_pdb  
(serial_numbering == "h36"), polymeric_res_names)  
  
See log for complete Python traceback.  
  

> save2 "C:/Users/Lenye/Desktop/PhD_2021/Rational protein
> engineering/H71/F57Y.pdb"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1373, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 90, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 101, in show_save_file_dialog  
_dlg.display(session, session.ui.main_window)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 31, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 60, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\pdb\\__init__.py", line 89, in save  
pdb.save_pdb(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\pdb\pdb.py", line 119, in save_pdb  
(serial_numbering == "h36"), polymeric_res_names)  
OSError: Unable to open file 'C:/Users/Lenye/Desktop/PhD_2021/Rational protein
engineering/H71/F57Y.pdb' for writing  
  
OSError: Unable to open file 'C:/Users/Lenye/Desktop/PhD_2021/Rational protein
engineering/H71/F57Y.pdb' for writing  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\pdb\pdb.py", line 119, in save_pdb  
(serial_numbering == "h36"), polymeric_res_names)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 431.90
OpenGL renderer: GeForce RTX 2080 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Acer
Model: Predator PT515-51
OS: Microsoft Windows 10 Home Single Language (Build 19042)
Memory: 17,098,264,576
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz"

[pett]

Hi Lenye,

You should upgrade to the latest ChimeraX production release. There have been hundreds of improvements since the 0.93 release that you're using, with several having to do with saving PDB files. Nonetheless, you should check the "usual suspects" for this failure: there is no pre-existing file by that name that you can't overwrite; the folder you are trying to write into exists and you have the right permissions to create a file in it; that you are not out of disk space.
If you upgrade to the current release and have the same problem, please report it. We will have a much better ability to track down the problem if you are using a recent version of the ChimeraX code.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab