Frequently Asked Questions
General
What file formats does Clavis support?
What file formats does Clavis support?
Currently, Clavis supports GROMACS
.gro files. Support for additional formats (PDB, XYZ) is planned.How many frames can I analyze?
How many frames can I analyze?
Free users can analyze up to 50 frames per month. Pro subscribers have unlimited access.
What is the difference between TRACE and HTR?
What is the difference between TRACE and HTR?
TRACE provides complete cage detection with face signatures (e.g., 5¹²6²). HTR focuses on ring enumeration and is faster for large systems.
Analysis
What H-bond cutoff should I use?
What H-bond cutoff should I use?
The default 3.5 Å (0.35 nm) works well for most hydrate systems. For high-pressure conditions, you may need to reduce this value.
Why are some cages labeled as 'incomplete'?
Why are some cages labeled as 'incomplete'?
Incomplete cages (IC) are partially formed structures missing some H-bonds. This is common at interfaces or during formation.
How long does analysis take?
How long does analysis take?
Typical analysis times:
- Small system (under 5,000 atoms): 1-2 seconds
- Medium system (5,000-20,000 atoms): 5-10 seconds
- Large system (over 20,000 atoms): 15-30 seconds
Account & Billing
How do I upgrade to Pro?
How do I upgrade to Pro?
Click your profile icon and select “Upgrade to Pro”. You’ll be redirected to Stripe for secure payment.
Can I cancel my subscription?
Can I cancel my subscription?
Yes, you can cancel anytime from your account settings. You’ll retain Pro access until the end of your billing period.
Do unused frames roll over?
Do unused frames roll over?
No, the free tier quota resets at the beginning of each calendar month.
Technical
Is my data stored on your servers?
Is my data stored on your servers?
No. Clavis processes files in memory and discards them immediately after analysis. We do not store your structure files.
Can I use Clavis offline?
Can I use Clavis offline?
Clavis is a cloud-based service and requires an internet connection. We’re exploring options for local deployment.
Path Tracer (PRO)
How do I access path-traced rendering?
How do I access path-traced rendering?
Path-traced rendering is available to PRO subscribers. Go to the RENDER tab in the right panel to access path tracer settings.
Why is my render noisy?
Why is my render noisy?
Increase the sample count. For noise-free images, use 256+ samples. You can also enable denoising for faster results.
How do I use depth of field?
How do I use depth of field?
- Enable “Depth of Field” in the RENDER tab
- Click “SET FOCUS” to enter focus mode
- Click on an atom to set the focus point
- Drag vertically to adjust the aperture (f-stop)
- Lower f-stop = more background blur
How do I reposition the light?
How do I reposition the light?
- Click “SET LIGHT” to enter light positioning mode
- Click anywhere in the 3D scene to set the light direction
- The light will point from your click position toward the scene center
What's the difference between DEFAULT and OSPRAY presets?
What's the difference between DEFAULT and OSPRAY presets?
- DEFAULT: Glossy materials with realistic reflections, good for presentations
- OSPRAY AO: Matte ambient occlusion style, cleaner look for publications