Opened 2 years ago

Closed 13 months ago

Last modified 13 months ago

#9404 closed enhancement (fixed)

'center' arg when opening small molecules

Reported by: Tristan Croll Owned by: pett
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc: Elaine Meng, Tom Goddard, Tony Schaefer
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
When opening some models (particularly small molecules from file or SMILES) it would be really handy to have an optional argument on the command that shifts them to a user-specified point (or the center of rotation) on opening. E.g.:

open C1=C(Cl)C=C2C(=C1)C=C(C(N)=O)C=C2 from smiles center 150,150,150

or

open C1=C(Cl)C=C2C(=C1)C=C(C(N)=O)C=C2 from smiles center cofr

OpenGL version: 3.3.0 NVIDIA 518.01
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_GB.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: HP
Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 34,007,068,672
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-GB

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Change History (9)

comment:1 by pett, 2 years ago

Cc: Elaine Meng added
Component: Unassigned → Input/Output
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → 'center' arg when opening small molecules
Type: defect → enhancement

comment:2 by pett, 2 years ago

Elaine and I have discussed this and feel that the two palatable options are:

(1) Offer it only for formats where the input coordinates are somewhat arbitrary. Off the top of our head: SMILES, PubChem, and IUPAC.

(2) Add 'cofr' as a possible value for the 'move' command. The downside for your scenario is that you would need to know the model number of the new model in order to issue the right 'move' command.

Thoughts?

comment:3 by pett, 2 years ago

Status: accepted → feedback

comment:4 by Tristan Croll, 2 years ago 

Of those two, I personally like option (1) better... but would it make more
sense as a general option if the argument was called something like
"shiftTo" rather than "center"?

On Fri, Jul 21, 2023 at 9:58 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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>
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comment:5 by pett, 2 years ago

Cc: Tom Goddard added
Status: feedback → accepted

Discussed this with Tom and he felt this would be of some general utility. For instance he often wants a structure opened in/near a map regardless of the structure's builtin coordinate reference frame. So I guess I will implement it as a generic "center" argument to the "open" command, with the value being the same as a "point-spec" documented here: ​https://www.cgl.ucsf.edu/chimerax/docs/user/commands/pointspec.html#point, which already allows "cofr" as a value.

comment:6 by Tristan Croll, 2 years ago

Cc: Tony Schaefer added

Adding Tony Schaefer to the cc list, because I'd love to see this new option reflected in the SEQCROW 2D builder GUI. :)

comment:7 by Tony Schaefer, 2 years ago 

That should be pretty easy to do, though the 2D builder never calls the
`open` command. I just do `session.models.add([struc])` to avoid saving
intermediate files.

Tony

On Tue, Jul 25, 2023 at 2:48 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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>
>
>

comment:8 by pett, 13 months ago

Resolution: → fixed
Status: accepted → closed

Okay, there is now a generic 'center' arg to the open command that places the center of each open model at the specified center position. Useful for placing structure in maps, or small molecules on existing ligand positions, or with the upcoming kvfinder pocket-finding command.

Change: ​https://github.com/RBVI/ChimeraX/commit/2ac2019da96ad591e2e1e7c39f31245cfdd3a6e2

comment:9 by pett, 13 months ago

"...open*ed* model..."

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