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Opened 5 years ago
Closed 5 years ago
#3425 closed defect (duplicate)
RFE: command to add C-terminal oxygens
| Reported by: | Tristan Croll | Owned by: | Eric Pettersen |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | Elaine Meng | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description I just put this together as a script to go in the ChimeraX presets directory, to help Dirk Fahrenkamp who was asking about how to add C-terminal OXT atoms to chains in his (very large) model. I know AddH will do this when it knows from the provided sequence that a residue is actually C-terminal, but as far as I'm aware there's no existing tool to do it manually. Anyway, it might be nice to implement something like this as a command? Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 3io0 format mmcif fromDatabase pdb 3io0 title: Crystal structure of EtuB from Clostridium kluyveri [more info...] Chain information for 3io0 #1 --- Chain | Description A | EtuB protein 3io0 mmCIF Assemblies --- 1| author_and_software_defined_assembly > preset custom "add oxt" > open /home/tic20/chimerax_presets/add_oxt.py No atoms selected! > show > hide cartoons > select /A:303@CA 1 atom, 1 model selected > preset custom "add oxt" > open /home/tic20/chimerax_presets/add_oxt.py Selection must be from a single model! > preset custom "add oxt" > open /home/tic20/chimerax_presets/add_oxt.py Traceback (most recent call last): File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py", line 1027, in <lambda> run(ses, "preset %s%s" % (cat, StringArg.unparse(name.lower())))) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/preset_mgr/cmd.py", line 49, in preset_cmd session.presets.preset_function(cat, matches[0])() File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/preset_mgr/manager.py", line 89, in <lambda> name: lambda p=preset: self.execute(p) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/preset_mgr/manager.py", line 68, in execute preset() File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/preset_mgr/manager.py", line 109, in <lambda> run=run, ses=self.session: run(ses, "open " + p, log=False) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 101, in cmd_open Command(session, registry=registry).run(provider_cmd_text, log=log) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 152, in provider_open name or model_name_from_path(fi.file_name)), provider_kw) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 365, in collated_open return func(*func_args, **func_kw) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core_formats/__init__.py", line 48, in open return open_python_script(session, data, file_name) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/scripting.py", line 82, in open_python_script _exec_python(session, code, argv) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/scripting.py", line 59, in _exec_python exec(code, sandbox.__dict__) File "add_oxt.py", line 25, in <module> NameError: name 'add_oxt' is not defined NameError: name 'add_oxt' is not defined File "add_oxt.py", line 25, in See log for complete Python traceback. > preset custom "add oxt" > open /home/tic20/chimerax_presets/add_oxt.py Traceback (most recent call last): File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py", line 1027, in <lambda> run(ses, "preset %s%s" % (cat, StringArg.unparse(name.lower())))) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/preset_mgr/cmd.py", line 49, in preset_cmd session.presets.preset_function(cat, matches[0])() File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/preset_mgr/manager.py", line 89, in <lambda> name: lambda p=preset: self.execute(p) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/preset_mgr/manager.py", line 68, in execute preset() File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/preset_mgr/manager.py", line 109, in <lambda> run=run, ses=self.session: run(ses, "open " + p, log=False) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 101, in cmd_open Command(session, registry=registry).run(provider_cmd_text, log=log) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 152, in provider_open name or model_name_from_path(fi.file_name)), provider_kw) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 365, in collated_open return func(*func_args, **func_kw) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core_formats/__init__.py", line 48, in open return open_python_script(session, data, file_name) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/scripting.py", line 82, in open_python_script _exec_python(session, code, argv) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/scripting.py", line 59, in _exec_python exec(code, sandbox.__dict__) File "add_oxt.py", line 49, in <module> File "add_oxt.py", line 24, in add_oxt AttributeError: 'str' object has no attribute 'chain_id' AttributeError: 'str' object has no attribute 'chain_id' File "add_oxt.py", line 24, in add_oxt See log for complete Python traceback. > preset custom "add oxt" > open /home/tic20/chimerax_presets/add_oxt.py Added a C-terminal OXT to chain A executed add_oxt.py Preset implemented in Python; no expansion to individual ChimeraX commands available. > close > open 3io0 format mmcif fromDatabase pdb 3io0 title: Crystal structure of EtuB from Clostridium kluyveri [more info...] Chain information for 3io0 #1 --- Chain | Description A | EtuB protein 3io0 mmCIF Assemblies --- 1| author_and_software_defined_assembly > show atoms > hide cartoons > select /A:304@N 1 atom, 1 model selected > preset custom "add oxt" > open /home/tic20/chimerax_presets/add_oxt.py Added a C-terminal OXT to chain A executed add_oxt.py Preset implemented in Python; no expansion to individual ChimeraX commands available. > select /A:304@OXT 1 atom, 1 model selected > delete sel > show cartoons > hide cartoons > cofr centerOfView showPivot true > select /A:303@C 1 atom, 1 model selected > show sel cartoons > select clear > show cartoons > hide cartoons > select /A:304@C 1 atom, 1 model selected > preset custom "add oxt" > open /home/tic20/chimerax_presets/add_oxt.py Added a C-terminal OXT to chain A executed add_oxt.py Preset implemented in Python; no expansion to individual ChimeraX commands available. OpenGL version: 3.3.0 NVIDIA 440.33.01 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision T5600 OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Cache Size: 20480 KB Memory: total used free shared buff/cache available Mem: 62G 3.5G 50G 99M 8.9G 58G Swap: 4.9G 0B 4.9G Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1) Subsystem: NVIDIA Corporation Device [10de:11df] Kernel driver in use: nvidia PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 File attachment: add_oxt.py
Attachments (1)
Change History (7)
by , 5 years ago
| Attachment: | add_oxt.py added |
|---|
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Structure Editing |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → RFE: command to add C-terminal oxygens |
comment:2 by , 5 years ago
| Status: | accepted → feedback |
|---|
So is the idea that you are unwilling to add hydrogens to this model for some reason?
comment:3 by , 5 years ago
Not exactly. The user (Dirk) had already run AddH, but it didn't add OXTs because it didn't know which C-termini were real (in an enormous model with many chains). In general it wouldn't be a good idea to do a blanket "add OXT to all chains", so having a more precise "add OXT to *these* chains" would be useful. On 2020-06-22 17:50, ChimeraX wrote:
follow-up: 3 comment:4 by , 5 years ago
This kind of sounds vaguely like an AddH problem, but I'm still confused as to how AddH wouldn't "know which C-termini were real". Possible scenarios are:
1) SEQRES records (or equivalent) are correct. Actual termini should get OXT.
2) No SEQRES-equivalent information. All termini will be treated as real and get OXT.
3) Incorrect SEQRES info.
a) Completely incorrect and does not match chain sequence. Info will be discarded and work the same as (2)
b) Sequence matches but is incorrect. Only in this case could some real termini not get OXT.
But you don't seem to have scenario 3b since in that case the final residues of the problematic chains would be None and the code you supplied would fail.
So I guess I need clarification about AddH not knowing which C-termini were real.
comment:5 by , 5 years ago
Hmm - actually, sounds like it might be my understanding that’s faulty. The problem is, this isn’t my model (and I’ve never actually seen it) so I can’t say exactly what’s going on. He’s happy with the script I sent him, so there’s no urgency. Perhaps this could simply boil down to the existing RFE ticket to allow fine-grained application of AddH to a specific selection of residues. Kill two birds with one stone. ;)
follow-up: 5 comment:6 by , 5 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | feedback → closed |
Hmm, okay. Restricting AddH to a selection is ticket #2310.
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