Troubleshooting¶

I cannot tell whether I have unsaved work¶

Look at the toolbar Save button. If it is greyed out, everything is committed. If it is active, File → Commit. The Parameter Explorer saves separately and is not covered by that button.

A colleague's model is not in my list¶

Access is per model. The Filter by control at the bottom of the Models browser starts on Recent Models; switch it to All Models. If the model is still missing, ask them to share it — models are private to their owner until shared or made public.

A panel has gone, or I cannot find the Outline or the Notes¶

Nothing is lost. Every panel has a button in the bar along the bottom of the window and an entry in the View menu; click either to bring it back. A panel with nothing to show — the Outline with no tab open, Notes when only a MOE is open — leaves the screen by itself and returns when it has something, and its button's tooltip says what it is waiting for. View → Layout → Reset Layout puts everything back where it started, sizes included. See Arranging the panels.

The search box does not seem to find anything¶

Results appear in the Search Results panel on the right edge, beneath the box, as you type. A single character matches only the start of a name; from two characters on, any part of it. The panel shows the first hundred matches and offers the rest with Show more….

My equations do not match my diagram¶

The equation listing is derived and rebuilt on demand, never silently. A banner above it says so; press Regenerate. See Keeping the equations current.

Regenerating says the realization is incomplete¶

Some processes have no rate law, or some states no initial condition. ProcessDB refuses to generate equations with undefined symbols, and offers to Fill defaults & continue. The Action Items panel opens along the bottom of the window whenever a realization has blank rows, highlighted at the top; fill them in there, or accept the offer.

The Simulate button is greyed out¶

The equations or parameter values are still loading from the database. It enables itself after a moment.

My data does not appear on a graph¶

Almost always a measurement with no Variable set. Open Edit Associations and Weights in the Parameter Explorer, or the experiment's measurements table, and set the model variable each measurement corresponds to.

The other possibility is that the variable name no longer exists — the state was renamed, deleted, or belongs to a different experiment than the one you are plotting.

The simulation will not converge¶

The solver reports the failure and still sends partial results to the graphs, so look at where the curves stop. Then:

1. Open Inspect Simulation, set a plausible minimum and maximum for state values, and find the variable that leaves the range — a concentration heading negative or a flux running away is the usual culprit.
2. Check that parameter's value and its bounds. A rate constant many orders of magnitude too large makes the system too stiff to integrate.
3. Check for a division by a state whose initial condition is zero.
4. If the model is genuinely stiff, loosen the tolerances from the Tolerances toggle.

An equation line reads something = 0 and I do not recognise the name¶

The generator emits a placeholder when a formula refers to a symbol nothing defines. The usual cause is a rate law naming a state that has since been deleted from the model. The Action Items row for that rate law is highlighted and its tooltip names the missing state: re-derive the law with Default… or Fill Defaults, or put the state back.

A parameter I want to fit is not in the list¶

It is probably defined by a rate law that is not the active one for its process. Open the process's Edit Rate Law… dialog and check which law has its Active box ticked.

A MOE function's parameter will not take what I typed¶

The Value cell holds a number: an integer, a decimal, or scientific notation such as 1.2e-3. It turns red while the text is not one, and cannot be left blank — press Esc to keep the previous value.

The optimizer reports many failed evaluations¶

The search is entering regions where the model will not simulate. Tighten the Lower and Upper bounds, tick Log for parameters spanning orders of magnitude, and reduce how many parameters you are fitting at once. Find Potent Parameters tells you which ones the data can actually determine.

The fit looks good numerically but wrong on the plot¶

Check the weights. Unweighted least squares lets your largest measurements dominate completely; 1/value² is usually a better choice for concentration data. See Weights.

A parameter came back sitting exactly on its bound¶

The optimizer is telling you the bound is wrong, or that the data wants something the model cannot provide. Widen the bound and refit; if it runs away, the mechanism is probably what needs attention, not the number.

My diagram is an unreadable hairball¶

Mask the ubiquitous cofactors — ATP, ADP, protons — with Mask State(s), then turn on the State Mask toggle. Group the parts you work on into subdiagrams, and use Layout to rearrange.

The exported bundle is missing the diagram or the plots¶

Both are taken from what is on screen. The diagram is exported only while the model's diagram is open — from a MOE tab alone it is not — and a graph only while its window is open. Open them and export again; the report lists anything it had to leave out. See The model bundle.

ProcessDB stopped unexpectedly¶

Relaunch it. If you had uncommitted work, ProcessDB offers to recover it from its local journal before loading anything else. Accept the offer. See Crash recovery.

A save failed¶

Read the Save Report — it names exactly which objects did not persist and why. Fix what it names and press Save again; only the outstanding items are re-sent. If you cannot make it succeed, use File → Export Unsaved Changes… so the work can be recovered, and contact support.

Something else¶

The Help menu opens this documentation, and Help → About reports your ProcessDB version — worth including when you report a problem.