FAQ and privacy

What happens to the files I upload?

Files you upload to the web app are converted on the server and are not stored permanently. To serve your downloads, and to avoid converting the same file twice, the converted results are kept in temporary storage for up to a day and then deleted. They are not published or shared.

The one exception is optional. After a run with several drawings, the app may ask Which drawing do you prefer? If you answer, your choice is saved to help tune how CIFlat ranks its drawings. It is saved together with the preview images of the drawings you compared, the file name, the formula and the options used. Your structure file itself is not saved. If you would rather not share this, simply don't answer.

The web app needs no account. If you prefer that nothing leaves your computer, run the program locally (see Installing the program).

What input does CIFlat need?

A CIF with a unit cell, symmetry operators (or a space-group name) and atom sites. Occupancies and disorder labels are used when present. Hydrogen atoms are optional, and the sum formula is read only for the check. CIFs from the CSD, from the COD, or from your own refinement all work. The program also reads MOL, SDF and SMILES, which skip the crystallographic steps.

Do I need ChemDraw?

No. The CDXML file opens in ChemDraw, which is the most common reason to want it, but CIFlat also writes MOL, SMILES, SVG and PNG files. ChemDraw is a trademark of its owner; CIFlat is an independent program and is not affiliated with or endorsed by it.

Can I edit the drawing?

Yes; that is the point of the CDXML file. Open it directly to keep CIFlat's layout. A "clean up structure" command in the editor, or an import from SMILES, will compute a different layout.

Can I trust the result?

Read the status and the report. ready means every available check passed. needs_review means a warning was raised, and the report names it. invalid means an error was raised. Writing a file successfully does not establish that its chemistry or its drawing is correct. The limitations and the measured results say how far each part can be relied on.

Why does the drawn formula differ from the deposited one?

Usually because of the file. Solvent may have been removed from the model, solvent or counter-ions may be partly occupied, a site may be shared by two elements, or the formula may be written for another Z. Sometimes it follows from a convention for partly occupied groups. The formula check attributes every atom of difference to named sites, and the interpretive cases explain each situation.

My structure is a polymer. What will I get?

A chain is drawn as one repeat unit in square brackets. A sheet or framework is drawn as an excerpt, with each cut shown as a wavy bond to a ghost of the atom beyond it. You can ask for more repeat units, or for the whole assembly. Polymers are always returned as needs_review, because an excerpt is drawn.

Why does a structure take a minute or more?

Most of the time goes into the layout search, which tries several starting layouts and untangles them against the drawing rules; see how it works. The hosted app runs on a free CPU tier, so polynuclear and heavily disordered structures take longer. The default budget is 45 s of search per fragment, and the web form lets you change it.

Will I get the same drawing every time?

Yes, with the same input, options, seed and software versions, when the compiled layout core is used, as on the hosted app. The search deadlines are then counted in work done, not read from the clock, so a slower machine takes longer instead of drawing something different.

Is there a desktop version?

A desktop program, in which all reading, perception and layout run on your own computer, is in preparation.

Where is the source code, and what is the licence?

[source code location to be announced]; [licence to be announced].

How do I report a wrong drawing?

[contact address to be announced]. Please include the CIF (or its CSD or COD identifier) and the report file.