id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4996 Can't write PDB file DLMLEN001@… Eric Pettersen "{{{ 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 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 *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 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 *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"" }}} " defect closed normal Input/Output can't reproduce all ChimeraX