RFE: Add a matchmaker option logParameters

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-15.3-arm64-arm-64bit
ChimeraX Version: 1.10.dev202503040129 (2025-03-04 01:29:19 UTC)
Description
Would be nice to have a matchmaker command option to suppress loggin the table of parameters used by the algorithm (logParameters false).  I rarely want to see all those default parameters and the useful info of the RMSD gets obscured by the large output.  Might be nice to make that option to not log the parameters the default.


Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202503040129 (2025-03-04)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 8yj9 format mmcif fromDatabase pdb

8yj9 title:  
Crystallization Studies of Concanavalin A in-Complex with D-Arabinose [more
info...]  
  
Chain information for 8yj9 #1  
---  
Chain | Description | UniProt  
A | Concanavalin-Br | CONA_CANBR 1-237  
  
Non-standard residues in 8yj9 #1  
---  
CA — calcium ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MN — manganese (II) ion  
ROR — L-ribose  
SO4 — sulfate ion  
  

> ui tool show Boltz

> boltz predict #1

Please cite Boltz-1 Democratizing Biomolecular Interaction Modeling. BioRxiv
https://doi.org/10.1101/2024.11.19.624167 if you use these predictions.  
Running Boltz prediction  
Running command: /Users/goddard/ucsf/boltz/boltz_venv/bin/boltz predict
/Users/goddard/Desktop/boltz_2/input.yaml --use_msa_server  

> open
> /Users/goddard/Desktop/boltz_2/boltz_results_input/predictions/input/input_model_0.cif

input_model_0.cif title:  
. [more info...]  
  
Chain information for input_model_0.cif #2  
---  
Chain | Description  
A | .  
  
Color input_model_0.cif by residue attribute pLDDT_score  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 2 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8yj9, chain A (#1) with input_model_0.cif, chain A (#2), sequence
alignment score = 1180.7  
RMSD between 231 pruned atom pairs is 0.358 angstroms; (across all 237 pairs:
0.782)  
  

> color bfactor #2 palette alphafold

Collection has bfactors  
1808 atoms, 237 residues, atom bfactor range 68.2 to 98.9  




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[Eric Pettersen]

Elaine feels that calculations with a bunch of parameters should normally log the settings used for reproducibility. So no problem creating a logParameters option, but strongly leaning to keeping the default true.

[goddard@…]

Ok.  I think almost all of our tools don't log their parameters.  But I'll be happy just to have the option not to log them so when I invoke matchmaker from one of my tools I can reduce the output.

[Elaine Meng]

At least in my (ancient) experience running calculations in programs like DeepView and SYBYL, they would always log the adjustable parameters.  Not a whole force field, but other types of run parameters.  It's most important for things like hbonds and contacts that tabulate a list of results that can be saved to a file.  Matchmaker is kind of in the middle but people might wonder why they got a different RMSD, or different parts of the structures overlaid, than in some previous run on the same structures.

[Tom Goddard]

Our Log logs the command that did the calculation and usually that command reproducibly runs the calculation with all the parameters either as defaults or explicitly given as options. I guess sometimes the defaults could change in different versions of the program or the unpleasant situation where some hidden setting can change the defaults. Not sure either of those cases pertain to matchmaker. But I don't really object to too much logging except when it buries the results of my own tool (e.g. AlphaFold or Boltz) that wants to use matchmaker as one step in its calculation.

[Elaine Meng]

Is this option just in the command, or will there also be a setting in the GUI?

[Eric Pettersen]

It will be in both.

[Eric Pettersen]

There is a "logParameters" command keyword now, and an option under the "Fitting" tab of the tool. Both default true.